Restoring APKs + data from 4.1 to 4.2.2 I migrated from Android 4.1 (Omega) to Android 4.2.2 (SuperNexus) on my Samsung Galaxy S3.

Before I did the migration I did a backup of apps with Super Backup. After this was done I moved all the files from the SmsContactsBackup folder to SDCard.
After flash, I've installed Super Backup again from the Play store and putted the SmsContactsBackup folder in /storage/emulated/0/SmsContactsBackup. Now I see all the backups in the Super Backup app.

After I do a restore/install of an app, the settings are not being picked up by the apps.

Plague Inc.: I see the settings in data/data/com.miniclip.plagueinc. But the app crashes on launch.
Lazors: I see the settings in data/data/net.pyrosphere.lazors. But my progress is gone.

Do they need to be somewhere else? Or do I need to use some other tool which can use my previous backups
Essentially, for backing up apps or SMS, TitaniumBackup works wonderfully. I've always relied on it to get my job done. But since you've already backed up your apps, I'd suggest you to try moving your app data folder to storage/emulated/0/Android/data/ folder instead of where it is now, and if it is a .obb folder, move it to /Android/obb. It'll pick up your settings.