Audio problem solved!!!.
I returned my 21.5" Imac with fusion drive and exchanged it for one with a 500GB SSD. Everything now works perfectly. I've spent the last 3 x days testing my Apogee Duet Firewire and RME Babyface USB. No clicks, pops, static. Recorded guitar and vocals using Logic. Left logic running on a loop for a few hours. Spotify, iTunes, Youtube through Safari all play and sound great. None of these things worked for more than a few minutes (if at all) on the iMac with Fusion drive. I'm running 10.9.1
It's taken endless calls to Apple Care and numerous emails to Apogee and RME over the last 2 x months. I took the iMac to the Apple "genius" people and they said they'd had similiar issues. They made a note in the Applecare documents that this imac wouldn't work with Audio devices and suggestred it be changed. I paid the upgrade costs ($360) for the SSD model.
I'll never buy the latest untested computer again. I'd heard people say you should always wait and let other people do the testing but I probably got sucked in by the glossy ads. Newer, bigger, faster is better right?
Apple should be warning people who are buying these machines for audio production that there are major issues. I spent $2600 on a machine that wouldn't do what it said it would. I then spent $800 on an RME Babyface because I was told it was an external audio issue. Then paid $360 to upgrade to to SSD.
Don't mean to rant. I just hope someone reads this before buying an Imac with Fusion drive. But then again why would you read this first?