Leak between Foam Liner/tray and Drain hose

[thstone]

From your description of the problem, my first instinct is to wonder about a crack in the foam liner. This would create the same situation as you theorize where water gets between the foam liner and the fenderwell drain but does not go down the drain line. This might be more likely if the painter removed any portion of the foam liner during the paint job.

[Meir]

hi gunman.
there is another drain hole that is very hard to find.
its located at the end of the clam-shell rail.
see yellow arrow (took me 3 months to find it )
not sure it will solve your problem, but it needs to be clean.