Marc, do you enable the low / ultra low latency mode on your iPad Mini / iPod Touch?
I use the low latency mode, as opposed to the ultra-low mode.
There's a bit of a story behind this.
Some months ago, before one of the JamUp updates, I guessed (but didn't test, so I'll make up some numbers) that the Round-Trip Latency (RTL) was, say, 18ms in low, and 9ms in ultra-low so I used ultra-low... and all was well with the world. No clicks or pops.
Along came an update that decreased the two latencies to 10ms RTL (which I have tested) in low, and (I'll guess) 5ms in ultra-low. Suddenly, there was clicking and popping in ultra-low, even on the newer Retina iPad. This clicking issue caused a s**tstorm among users for a couple of weeks. PG claimed a fix and sent out an update. It seemed to help a bit but, in my case anyway, didn't completely stop the problem. All along, until that point, I didn't realize that latency was the issue - PG didn't mention that they had changed the RTL values.
I figured it out when I realized that I could get the same problem on my desktop and laptops by decreasing the number of samples. So... to make a long story even longer - I tried low mode and, lo and behold, the problem went away.
Whereas as before I had found low to have an uncomfortable RTL - unplayable, really - suddenly low was fine but ultra-low was causing me problems. I have left it in low on both iPads (and my new iPod) ever since.
To be honest, 10ms is low enough for me not to feel the latency, so I'm more than OK with the way things are now. Someday, if the processor power can catch up (on a future iPad) I may try ultra-low again. But as things are now, I could live happily ever after. And that's my story.