Generally, Forced Streams are the subtitles (or subpictures) that need to be displayed when languages changes, such as Japanese in an otherwise English movie. However if you elect to remove all subpicture streams, there is a good chance this will over-ride the Forced Streams option and leave you with no subtitles at all.
There could be a couple of factors at play here.
1) Some players, if you set the subtitles to English in the setup menu, turn on the English subtitles on every movie, whether they are forced or not. Annoying, but I have seen (and owned) several that do this. If this is happening a lot, even with commercial discs, check the player.
2) If it is only hapening on backups then the process or tools are at fault. Test play the files from disc before you burn and try to isolate the culprit. It would help to know what tools you are using.
3) Current copy protection is getting to the point where weird things are happening to backups. There has been at least one instance reported of subtitles being turned on following a standard rip exercise, simply because the disc structure is now so screwy.