Logic Mainstage Guitar Patch Problems

Hi, please help! I've been using Garageband for 12 moths or so and have some real killer patches set up. Up to now I've been just using my MacBook I/O sockets.

A few weeks ago I purchased an Apogee GIO and Logic 9 (full version)

The install all worked successfully but using the Apogee GIO Guitar Input ALL guitar patches in Garageband Logic and Mainstage sound really awful! thin/wooly/trebly/hollow just plain YUK!.

The output from the GIO sounds great using any loops in (GB L or MS) or Itunes or DVDs. Thing is Both Logic and Mainstage guitar patches sound awful when using the MacBook line-in too.

However last night I was trying again and just using the MacBook I/O and I managed to create a really great clean chimey patch in Mainstage (the first decent sound I've managed to get out of it) The really weird thing is when I saved it and then used the very same patch in Logic it reverted to a dull and yucky sound again.

I'm now at a complete loss now - It must be some kind of set-up issue but I for the life of me can't see it.

Any help would be greatly appreciated

Cheers