Good thread. I have a few--
I've noticed, that when recording opti-in, if I leave it in pause for awhile, that the channels will swap when you unpause. This is unverified by anyone but me right now, but I suspect it's a global problem. I started a thread about it awhile back.
Thread here.Rereading that thread reminded me that people have had issues with the meters swapping without the channels swapping.
Not really related to taping, but I've had problems when transferring mp3's to my jb3. Notmad will act like it's transferred the file, but the file won't be there. And then it does the same thing to any following mp3's--it will act like it's transferred the files in a fraction of a second, but nothing there. According to Notmad's Omnitome, there are mp3 files that the jb3 has problems with, though it says you will get an error message (I got no error message). In short, be aware that there are random mp3's that just won't transfer to your jb3.
Also, to support what bean said, I've had problems after formatting the jb3. When you feel the need to reformat, be near your computer with the current firmware ready to go. And make sure you power down/reboot a few times to make sure it's running smoother, maybe even do a test recording.
These aren't things to keep you from happily taping with your jb3, merely idiosyncracy's.