It might still be worthwhile to try a driver reinstall. Not because the driver is incompatible with win98se, but because it might have somehow gotten corrupted.
If you watch posts in this forum for awhile you see a lot fussing about 95-98 degrading over a period of time.
That may not be your experience and it may not be the cause of your problem, but I'd think it would be worth a try.
If the other printing that is normal is all less than 10 pages, I suppose you could also try removing the parallel port and letting it reinstall that-on the same theory-that some how the driver might have gotten corrupted.
you could also run the system file checker and see if it shows spooling programs corrupted.