It could be the Windows 2000 write caching feature. On WIndows 2000 it isn't until you close the files that windows will start to save the database to the disk, so maybe it is this saving process that you are waiting for?

The only reason I say this is because I don't think write caching is available on Windows 98? You could test this by turning off the Write caching on the windows 2000 machine.

Chris.