I've found almost always that my JB3 has an error of something like 2.5 samples/sec at 44.1
So you run analog-in to the JB3? What was your control device?
One matrix I did was set up like so:
SBD: Mono out from the board into MZR-700 MD in mono mode, transferred analog in to my PC thru M-audio Delta 1010LT analog-in.
AUD: Wmod UA-5 optical->JB3
...So I guess I misspoke. The error is probably coming from the MD. Not surprising. But I also noticed a similar (but not exactly the same) discrepancy when doing the same thing with 1 source being a Laptop and the other a JB3. If I had a freaking MD deck with digital out I could make a better evaluation, but I'd rather not use the MD unless I absolutely have to.
Lately I've been bringing my luggable PC and doing a 4-track matrix in Sonar, then just clipping out the stage delay from the AUD side. Much better than having to resample and all.