I have A/B compared the Apogee mini-dac and the MDA1000 (also a few other DACs).
The Apogee sounds absolutely great. The only complaint I had was that it would drop the USB connection occasionally (I bet Apogee has fixed that by now).
I have ended up using the MDA1000. Might be purely my...
I have a closet full of DAC's and various interfaces - USB, Firewire, I2s, digital coax, wireless, etc.
I have ended up using optical cable from my Mac Pro to MDA1000. It sounds incredible.
You will love using the MacBook into the MDA1000!!
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It kind of sounds like the MDA1000 is having trouble locking onto a digital signal.
Try switching to a different source or squeezebox to make sure the problem is not the signal from there.
Could possibly be your interconnect also. . .
One thing I like about the MDA compared to other DAC's...
I have a bunch of the 20 amp panel mount Brickwall surge protectors.
Even if you are not interested in their products, they have a lot of great info on their web site regarding MOVs.
http://brickwall.com/