I've never experienced anything like digital noise in JamUp. However, when you export an amp from BIAS to JamUp, there is a noticeable drop in level. I'm not really sure what causes that. I have not found a way to adjust or monitor input level in JU like you can in BIAS - only output.
I did have some success (and fun) with the combo of BIAS/JamUp, and the GR-55 today.
I tried the GR-55's guitar out and the GR-55's normal line out (mono) into the Apogee Jam interface. With the guitar out, I really had to turn up the level of the COSM sounds source more than normal. Usually 50 seems fine, I pushed it up into the 80s. And then I also got the regular, expected GR-55 guitar out port noise on higher gain amps.
Hooking it up with the normal line out was better. No noise. And of course the bonus of being able to do something like put one of the 55s distortion pedals into the signal chain. Only downside is this would really limit the ability to use the 55 for its own things, in a live situation.
For that the guitar out seems most appropriate. JamUp and BIAS both have noise gates so it should be doable. Still need to try this with the Alesis IO Dock which is what's been going on stage with me lately. Hopefully it will work with the iPad Air even though the case might not fit it perfectly. Wonder if anyone's coming out with a musical dock for this model. Thought I heard Behringer was going to make one with a lightning connector though I'm not sure they ever did...