There is a sad thing, the 96-00 Civic's, specially the coupes are notorious for the windows popping out of the track. The problem is that over time, without being lubricated properly, the rubber track that the window rides down on closest to the fender side of the door tends to buckle basically. This allows the window to start creeping out of the track.
You will notice the it when the window seems to go up or down slower than normal. Now that is the tricky part as you drive your car daily and its hard to notice small changes from day to day, where as if one day it was moving at half the speed you would notice it right away but if it takes 4 years to get to that speed, your already used to it.
Back on track though, once this happes, the modling itself will no longer hold the proper shape. Doesnt matter how many times you lubricate it, its only a temp fix and might not even work then. The solution is to replace the track itself. I have had to replace both my drivers and passenger track on my 99 that has 85k miles. Dealers charge about 140 for parts and labor. Some of you might wanna attempt it yourself, me, I have big hands and working in that door panel pisses me off to no end and 140 bucks is well spent to avoid the frustration and headache for me.