The issue is with packages that contain services and accounts. Basically you should copy the whole /media/cryptofs/apps/usr/palm folder.
I don't know what IPK Packager can do... but palm-package can be used to create IPKs for those more complex apps. Basically for each folder in packages do this:
1. Open the packageinfo.json in text editor
2. Note down the id (should be identical to the folder in packages)
3. Note down the name after "app" without quotes
4. Note down name after "services" without brackets and quotes
5. Note down all entries after "accounts" (yes, this can be multiple).
6. Open a command line on your PC (after copying all folders)
7. Browser to the folder where you copied all contents from /media/cryptofs/apps/usr/palm
8. For each app run this command line:
palm-package packages/<id> applications/<app> services/<service> accounts/<account1> accounts/<account2> ...
Leave away things you did not find. Also add all accounts.
You will need to have the SDK installed (3.0.5 is fine for phones, too). And you will need to add the folder with palm-package stuff to your path.
If an app has no folder in packages, then the above method is sufficient. But if there is a folder there, you will b e missing a service or account and the app probably won't work if installed on a fresh device. So be sure to doulbe check the packages folder.
In fact, you probably don't even need to create the IPKs. It is sufficient to just copy the folders, keep them, to reinstall copy them to device again and reboot. All the apps should show up and be properly configured (not 100% sure about the last thing).