Have had difficulties in the past with an Epson SCSI (flatbed) and Win98SE
Ignoring XP since this is 98 you are using for the Filmscan - What is showing in Device Manager, any yellow ! or ?
I think it might help to uninstall the Epson software. Have the scanner connected and On throughout the rest of this. Then "remove" anything showing yellow in Device Manager. Reboot and go through the "found-new-hardware" routine prompt by prompt (but not actually offering the Epson CD) until Windows gives up looking and says it can't find the software.
Now at last run the Install CD and accept SCSI as the one to use. At the end of the installation reboot and pray. I believe you can then on using Acquire in the application, select Epson Twain or Twain32 and you're in business.... I hope.