That's very strange indeed that it won't show you your Library. Especially since we've run the program with much larger test libraries here. Could you please send us the crash report for Pocketpedia so we can look into that here? After you sync your mobile device all crash reports will appear in ~/Library/Logs/CrashReporter/MobileDevice/[your device name]/ under the name "Pocketpedia…crash".
Also, could you please send us your Database.dvdpd file so we can try to reproduce the problem here, just in case there's something unique to your database. You'll find the file in your Home folder under ~/Library/Application Support/DVDpedia/Database.dvdpd. Please archive the file before sending it to save space. (Select it and choose 'Archive' or 'Compress' from the File menu. That'll create a new file called 'Database.dvdpd.zip' which you can then attach to the email.)
If you're on Lion, it hides the Library folder by default so to go to your DVDpedia data folder you have to use the Finder's 'Go' menu, hold down the Option key and the Library folder will appear.