We are having the same phone . However , my linked application will only experience force close when the sdcard was unable to be detected for some reasons during boot time . I've discuss with bakpinar and tried a lot of solution as well including fix permission , run a command , using root tools , rom manager and a more , but none of them seem to be work , so you don't have to waste time testing with the methods i've mentioned . However , recently i found an application named "root and me" . Well , i don't know what is that thing but in the description , it was written "*NEW UPDATE FIXES APP CRASH AND FIXES UNNECESSARY PERMISSIONS! DISREGARD COMMENTS!" . I haven't try with it yet . Perhaps you can try using that to FIX UNNECESSARY PERMISSIONS ? And if you have tried and it works , please let me know . If it doesn't work as well , you don't have to worry much because bakpinar is about to release a new version with multi-select function , maybe there is an option to reinstall (hope so) ?
I am not sure how "root and me" would help. But you are right. This happens anytime after the phone boots up without the SD card. Android would fail to find the apk and that's when they lose their permissions. It's strange how facebook continue to work.
Anyways, link2sd already has reinstall option, which works. It's just annoying if you use ADW to create custom shortcut, the shortcut goes away.
I am going to only link apps that work. And link apps that doesn't to /cache instead. BTW, linking large .so files to the sdcard using adb also saves internal storage.