Logic Pro/Itunes audio jitter

I recently moved from an old 2006 Mac Pro Tower to a new 2015 Mac Pro running the latest OS.

I have a recurring problem where the audio stutters/jitters severely when I'm running Logic, ITunes or Youtube. This is often when I'm running two at the same time - playing instruments or MP3's through logic and another song through iTunes or Youtube. This never used to happen on my 2006 MP.

the stutter get's quite bad, but stops if I mute everything, wait a few seconds and start again.

The computer is very high spec and the problem occurs even when running zero plugins - so I don't imagine it's underpowered. Since the MP has a very small onboard HDD, I'm also running an external Thunderbolt Lacie drive.

Sound card is an Apogee Ensemble w/ firewire/thunderbolt adapter.

Looking forward to seeing if you all can help me.