Logic Pro X Audio cutting in and out

When I am trying to record in Logic Pro X the audio seems to cut in and out at random points.
I have a MP3 track that I am recording to and it just randomly cuts out. Even when just playing that track by itself the same thing happens though never at the same spots. If I open the MP3 in Itunes or Quicktime there is no problem with the track.
As this seriously messes with the time of the piece and makes the recording long and painful I need help.
Is there some type of connection I am missing? I am using an old Presonus Firebox as an Interface, it unfortunately has adaptors to take it from firewire to thunderbolt. Recording into a 27" Imac that is very souped up and shouldn't have any problems until I hit a hundred tracks or so and I am only trying two.

It's most likely the Fusion drive, one of the symptoms is audio cutting out.
There are several related threads in this forum regarding audio problems with the Fusion drive.
This thread alone would take a couple of days to read.
https://discussions.apple.com/message/24709429#24709429
A fix is supposed to be coming in the next operating system update.

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