I don't know if this applies to you, but if you've rooted you phone and for whatever reason you're clearing the system cache partition then that'll cause the SE Token App to lose all its data and "reset" like you've experienced. Sadly because the token app stores its configuration in the cache and not the usual "data" location, it can't be backed up/restored by Titanium Backup (or similar) like other apps.

Also, if you receive an Android version update (to upgrade it to a newer version of Android), this may also wipe the system cache (breaking the token app in the process).

If none of this made any sense to you, then most likely that wasn't it and you should ignore my post, I was only mentioning in case you were doing something with the system cache like changing ROM etc so at least you'd know what was causing it.