for testing, make sure the 'system' option 'fast boot' is not checked.
the most common cause of the issue you describe is bad isos. Try using the iso in another emulator. I recommend using epsxe on the pc. Be sure to use the same iso - so I recommend you plug your phone into your computer and copy the iso to your computer and test. if it works - the problem is not the iso. if it doesn't work - probably the problem is your iso.
if the problem is not your iso, you can:
- try rebooting your phone (unlikely to fix - can't hurt)
- try uninstalling fpse, then reinstall fpse. After the latest update your memory cards and save states should not be affected. however, to be safe run a backup - menu, misc, backup - will save to /sdcard/fpsebackup.