The script didn’t ask a password for some rare FileOpen pdf combinations. This should fix (at least some of) the problems.
Reminder: The script* can’t decrypt FileOpen pdfs which need user authorization without the correct user/password or user/session cookie combination.
* In fact no other script can do that. You’re only chance to crack such a file is a brute force method. You can try with 40 Bit encrypted (V1) FileOpen pdfs but you have no chance in getting the key with 128 Bit (V2) FileOpen pdfs. More information about that topic can be found in the FAQs.