Two problems related to power window have been reported for the 1999 Honda Civic. The most recently reported issues are listed below.
My drivers side window slowed then came to a complete stop one rainy day while going through a toll booth. I was trying to close the window. It stopped halfway open or shut depending on your point of view. I brought it to my mechanic and took a peak while he repaired it. The clamps attached to the motorized track, that hold the window in place while moving up and down, had loosened up. The slack had cause the clamp to shift position during movement and the window in turn slid out of alignment. This caused the window to jam against the door frame. The last time this happened it was also during rainy weather.
While rolling driver's side window up with automatic button, window stopped approx 1/3 of the way from the top and wouldn't go farther; appeared jammed into the rubber around the window. Upon examination, found to be the window regulator.