If the old sealant is firmly attached it may be hard to get off. If it's essentially intact, I would simply caulk all around, including on top of the old stuff that remains. I would use a gutter and caulking sealant, probably a polyurethane.

HOWEVER, I'm not convinced that that is your problem. From the pictures it looks like the flashing is improperly installed. That vent should have the flashing boot on top of the shingles on the downside. The way that idiot put it in allows water to slip in around the hole through the shingles and get inside. To fix it properly requires that some of the shingles on the downside be removed and that the shingles go under the boot so that all the layers that are higher up lap over those below. This may be a job for a professional roofer if you don't understand completely what's involved and what you need to do so that all the layers are right and you also don't have exposed nail heads when you're finished. A second approach, which you could do is to caulk like crazy all around the pipe that penetrates the shingles so that the cut edges where the shingles meet the boot are completely covered by the caulking. However, this is a less than ideal approach: it may last for the season or for a couple of years. But, ultimately, you should get it fixed correctly. I would also examine all the other roof penetrations to see whether you have more problems like this.

Kudzu, thanks for the input, it's greatly appreciated. By the flashing boot do you mean the round piece of flashing that has clips on the side and meets the flat roof, or is it the flat piece of flashing that sits atop the shingles on the downside? There is a flat piece that's difficult to see in the pics. In any case I'll try to have it repaired by a professional roofer. The remodel was a project from hell with the GC putting his D grade subs on the job to save money because he underbid some expensive rock removal. It's a long, ugly story :-)

The part that is poorly sealed to the pipe is called a "storm collar" and you need to remove it and install a new one or put a new one above it. Sealant is only temporary and whoever put that sealant on the collar was only postponing the inevitable. Field expedient temporary repairs are only justified in a war zone.

Here is a link that might be useful: proper storm collar

zubini-
I looked at your pictures again, and I think I may have gotten misoriented the first time. If your picture at the right is looking at the vent from the top side and the upper right corner of the photo is further down the roof, then it looks like the flashing that goes over and under the shingles is installed properly...in the sense that the shingles above overlap it and it overlaps the shingles below. However, although it is hard to say from the picture, you may be getting lateral migration of water that is going sideways around the flashing. Macy is absolutely right, and I should have said something: that storm collar you have is way too small. It is possible that a decent size storm collar, properly installed and sealed, might prevent the leaking that is occurring, but I am still suspicious about whether the flashing on the roof for that vent is large enough and is installed properly, and whether the shingles around it are aligned properly to keep things dry. I am sorry if I originally misperceived the orientation of your photo, but I still think it's a good idea to get a competent roofer to look at it (and the other ones). Good luck. I'd be interested to hear how this turns out.

Thanks Macv & Kudzu. At least I have a better idea what's going on. What is the round piece that sits on the roof and under the shingles below the fluted collar piece - is that a type of collar also? You can see it has bendable clips on it that don't attach to anything. The fluted piece seems to just sit there not really doing anything. I so hate hack construction and yes, it was a type of war zone actually - and I was the defeated side :-)

Thanks again.

Sealant/caulk is commonly misused. It cannot seal anything if it doesn't fit between two relatively stable clean surfaces that don't move more than the material can stretch and still adhere. On the surface of another material it will simply become hard from UV exposure and crack. That goes for all sealant/caulks. They don't last forever even when installed properly in a joint.

When I first learned to detail building joints in the 60's, sealants and adhesives were not relied upon for weatherproofing. Everything had to shed water with a mechanically sound detail. That approach has been abandoned in favor of easy fixes that need frequent maintenance and many building owners have suffered losses because of it. Any time you are tempted to use a sealant/caulk you should first consider a more permanent solution.

In '71 our spec writer told us to stop using the word "caulk" and only use "sealant". In general, sealants are designed to seal a joint between materials that can move and caulks are designed to fill a stationary gap. I had to change the word caulk to sealant on a very large set of drawings and consequently avoid the word caulk unless it is part of a trade name.

In your case a stainless steel storm collar or a tight fitting neoprene gasket (preferably with a stainless steel compression band) are the only flashing details that will be permanent. That's assuming the base flashing cone has not split at the roof line seam.

All flashing should have a "base flashing" and a "counter flashing". In this case the base is a cone in a "witch's hat" shape, interleaved in the shingles and the "counter flashing" is the storm collar. Don't be tempted to use an "all-in-one" half metal and half neoprene "boot".

Macv, thanks so much for the info - you're a gem. None of the roofing companies I've called thus far are interested in even looking at it as they're all too busy. It could take a while to get this fixed properly but at least I'm on the right track.

zubini

The others are probably correct but just a thought. Did this leak only happen the one time "During the last huge rainstorm"

Was it windy that storm? Could the rain have blown into the vent? You also didn't say if there is a cap on the vent and your photos don't show one.

Our furnace and water heater are on the same vent stack and it is capped. One really bad storm, tornado sirens going off, my police scanner saying one on the ground...I love storms, but this one scared me. First time in my life I took the dog and went to the basement.

The vent stack was dripping rain, not because of a leak but because the sideways rain blew in under the cap. I worried so I put a Sunday paper under where the leak was. Six years later that paper is still sitting there on the utility room floor and shows no evidence of a leak.

You said "During the last huge rainstorm" maybe the rain blew in. OR if you don't have a cap on the vent, then of course the rain will get in.

The vent has been leaking for some time as evidenced by the sloppy glob of sealant where no sealant should be.

When you actually get up on a roof the story of poor repair and maintenance is as obvious as a pulp paper romance novel.

Thanks for your input Gammyt. The vent does have a cap and I thought about the water getting in from the windy deluge. The roof and venting is 5 years old and I've been through one other big storm like the last one and it didn't leak. I'm guessing when the roof/venting was installed over the course of a 1.5 year remodel it leaked due to the poor vent installation and the bleepty-bleep contractor put the goop on to stop any immediate leaking. They did so many things like this that they're guilty unless proven innocent. They probably couldn't find the proper collar at their local supply store so put on whatever was sort of close. If I told you some of the stuff that when on you truly wouldn't believe it. And this from a high-end contractor whose work has been on the covers of Dwell and Metropolitan Home so not usually a hack.