The most common leaks I've found on metal roofs are where there is a loose or popped nail or loose flashing. That much problem on a newer roof suggests a problem with the initial installation. I'd recommend getting an experienced set of eyes to look it over.

A small hole or improper flashing could be the cause. Can you get into the attic area to try to trace to the source? I have a metal roof and have had minor leak problems twice, both involving snow. In the first case, a huge snow storm put a lot of snow on the roof. When it started to thaw, the foot-deep mass of snow and ice put pressure on a vent pipe that snapped and provided an avenue for water to get in. In the second case, we had another snow and ice buildup on the roof and, when it started to melt, some of the ice created an ice dam that allowed water to pool and get up through one of the standing seams.

In addition to checking inside the attic for signs of leaks, take a look on the roof at areas where there are roof penetrations, like vent pipes, to make sure everything is well sealed. It only takes a tiny gap or break in the caulking to have water get in around a penetration.

ditto...check out flashings, penetrations & gaskets
on screws holding roofing down.
I often find bad gaskets...over tightened to where
they no longer seal, or so that they have split.
visaully inspecting these areas is a start.

go into the attic to see if you can determine where
leak starts by looking at roof decking.

water exits at low point, so leak can be higher
up that you expect.

best of luck.

Energy is bang on, you need to get into the attic, otherwise your looking for a needle in a haystack. Water migrates and a leak many feet away may show anywhere. need to find the source, then seal it form the exterior, not easy job in winter. Weather permitting a leak test with a garden hose starting at the roof peak is in my opinion the best way to test. One slowly sprays water from the exterior while one person is inside looking for where the water starts to show from the interior.

I don't know how old the roof is or if you had it installed but the big seller on metal roofing is the lifetime transferable warranty, is it possible it is warrantied?

I now see around these parts there are contractors offering a vinyl sealer sprayed from the exterior for older metal roofing, I'm sure it's not cheap. Best of luck.

Valleys on metal roofs sometimes cause problems if not installed properly. Water will rush down the roof on one side of the valley and up under the metal sheets on the other side.

This post was edited by bus_driver on Mon, Feb 25, 13 at 18:39

Agree re flashing, incorrect installation , screws etc. It's also possible the gutters/eavestrough could be full or blocked, and the water's backing up. I'd go up in the attic, turn out your flashlight, put hatch back down and let you eyes adjust, and look for light leaks, which might guide you to the leak.

I would avoid the spray-on vinyl thing - that's a half-assed fix that wouldn't last.