There should be weep holes in the track to allow water to drain.

If this water collecting is a continuous situation---happening even when there is no rain---the water has to come from inside the house. Condensation above the door, in the attic, or leaking plumbing on the second floor.

You first need to find the source of the water. That may mean removing sheetrock. If the cause of the water is not discovered and fixed, any damage will still occur.

One possibility just occurred to me. If the house is in a climate where there are extremes in outside temps, and there is a floor heating/AC register situated so that conditioned air blows on the door.

What that does is blow heated air on a cold door in the winter and cool air on a hot door in the summer. That will cause constant condensation on the door year round. And the condensation will drip into the channels. Depending on the inside/outside humidity and the inside/outside temperature differences, that condensation could be a sizeable amount in just 24 hours.

The test to see if this condition could exist? Simply deflect the air from the register away from the door. One of the plastic adjustable deflectors or just cover the half of the floor vent that blows air on the door.

No air blowing on the door---no condensation.

thanks for your thoughtful response. We're in a mild climate (north west coast) and we have electric baseboard heaters that are not far from the door but the heat goes into the room rather than onto the door. I haven't seen any condensation on the door or the window beside it, we don't have an upper floor (its a one storey house) and we have a new roof. So I am puzzled. We do have a lot of rain but we have a large overhang and don't get that much rain on the door. I can't find any weep holes in the track, do you know where they are located? thanks

If there is water in the inside tracks, it has to be coming from inside the house.

So, more questions.

Does the water collect regardless of rain?

Was this problem there before the new roof?

Is there any plumbing in the attic?

there is no plumbing in the attic
yes the problem was there before the new roof
yes the water does collect regardless of rain

It has to be condensation then. No other possible cause.

Easiest/cheapest way to find out is to buy/rent a de-humidifier and run it in a room with a slider. If that solves the water collecting in the cracks, you need to lower the humidity in the entire house or make sure conditioned air is not directed at the sliders.

One possible reason for the windows not being affected is the size of the sliders is attracting all the moisture.