Hmm... Here's what I would try.
- Put your old, working card in.
- Backup everything you would want to keep post factory reset, apps, SMS, contacts etc.
- Do a nand+ext backup, which means you're covered if this doesn't work.
- Switch to the new card whilst staying in recovery.
- Run the partitioning tool: SWAP: 0, EXT: (Up to you, I use 500), FAT: The remainder.
- Copy your backup files from the old card to the new card, as well as all of your other media files and so on, to fill up the card.
- Do a factory reset and wipe the dalvik cache
- Boot the phone and restore all your backups, including apps.
Then see if it works properly. It should, since you're starting from a clean slate.