This was quite a job.
My client called me over to look at the ceiling in a bedroom directly under the deck (see photo) the rock was bowing and dropping a bit. Upon investigation, the EPDM deck appeared perfect and functioning right. One of the windows (right side of photo) had some condensation from a broken seal, and aparently was completely rotten under the paint! Aparently this window had been wicking in water for so long, that alot of the framing around and under it was rotten... like top soil rotten!
I must say, for a window system installed in 1993, it really was done exceeding even todays standards! For start, everything was (still) plumb and level, an old butyl version of VyCor covered all nail flanges from bottom to top, the units were shimmed using plastic shims, and it wasnt over shimmed or over nailed. The only thing missing was a pan flash, and that is exactly why the water got in and the entire shoe rotted away. did i mention the extruded aluminum panels or the 3/8" bead of caulk holding them inplace??!
What we did was (when the new window arrived) take out the windows and door, replace all rotten lumber, and re-install the door and windows. it was alot of work for such a small leak, but it could have been worse! i really give Pella alot of credit for have installed this way back then, if not for a broken seal, this would all still be perfect.