This seems to be the exact problem I'm having, I really can't figure it out though.
I got my core and SID modules in the mail, stayed up late assembling them (and did a very nice job, I'm really proud of myself). I spent most of the next day troubleshooting but my original problem turned out to be my programmer wasn't programming the PIC18F4685's config bits properly, so after fixing that -- voila! MIOS Studio detected it, I was able to upload MIOS and then the SID application, and it worked! I used both my MIDI interface (the same one I used to program it over MIDI) and my keyboard to play music, which I had outputting through a small speaker just for testing purposes.
Great, I thought, it sounds awesome! I played around a bit, using SysEx to send new patches into the buffer (I'm going to install my BankSticks today) and everything was perfect.
I went to sleep, then today I sat back down to play around with it, and for the first few minutes it was sort of working... but then I noticed the MIDI IN light was flashing, as if it was in bootloader mode. So I opened up MIOS Studio, and yup -- it detected it, saying bootloader is up and running. So I scratched my head, shrugged my shoulders and tried to re-upload MIOS. It started to send it, but after a second or two it stopped with "Upload aborted due to error #11: MIDI IN Overrun Error". I fiddled around, trying to get it to work again, but no such luck. I do have two other 18F4685's so I tried blanking another one, burning just the bootloader (and getting the config bits right the first time!) and inserting it. This time it was definitely working in bootloader mode -- every second or so it sends it's ID or whatever byte it is to MIOS Studio, which immediately recognizes it... but I get the same error when I try to program it!
At first I noticed that when it was sending data to program MIOS there was also a bunch of data coming through in the MIDI IN window -- basically the same byte it sends when it's waiting for code to be sent to it, only much faster. Basically (it seems) every byte sent to it would trigger it sending that same byte back. However, I wasn't paying close enough attention when I first programmed it, so I'm not sure if this is normal or not. Two-way communication during programming seems to make sense, so this may be irrelevant, or it may be a symptom and not the problem itself.
I also spent quite a bit of time checking all my solder joints to make sure nothing was shorting out. But there can't be -- everything was working fine yesterday! That's what is really frustrating -- everything was working perfectly and I literally changed nothing -- just sat down and attempted to pick up where I left off last time...
Really not sure what I should do. Does anyone have more information about that error? Is it referring to the PC end or the Core end? Any and all help is appreciated. I've been trying to read all the info about troubleshooting the Core than I can, but I can't seem to find much on this problem.