Viper5,
there's been high thread traffic regards to the door lock mechanism and window operation.
Reported corrective action listed in this form spans from replacement of the lock mechanism, the switch on the outer door, bad spring in the mechanism, bad solder joint inside the door mechanism (my car) and worn window regulator.
my 2 cent, I suspect you are experiencing a worn window regulator - my car is doing the same now even after the re-learning process.
they say that the outer sleeve gets compressed, thus inducing a larger dead band where the motor does turn but percentage of the motor motion is taken up by the deadband (slop) and so the window does not lower enough.
normal window operation, i.e. full up, full down operator control motion is not affected.
You may want to perform quick testing outlined in the link below. & let us know of your findings. I may be plowing down the same path very soon.
good luck.
http://www.pelicanparts.com/techarticles/Boxster_Tech/77-BODY-Window_Regulator/77-BODY-Window_Regulator.htm
http://www.ppbb.com/phorum/read.php?19,1565400,1565407