Mega 2560 r2 and r3 uploading issues...any suggestions?

Problem: uploading programs to 2560 r2 and r3 stalls (most of the time...see below)
Environments tried: 0.22, 0.23, 1.0 and 1.0.1
Development platform: xp fully patched

I developed a project proto board that sits on top of the 2560. The protoboard is basically a 3 high speed counters. The 2560 uses one port (b) to simulate bus signals to the chips on the proto board, and uses another port (C) to read the data from the protoboard. The orginal configuration of IDE .22 + 2560 R2 used to upload OK, a little flakey at times but ok. Then uploads began to fail repeatedly, so I upgraded to R3 and IDE 1.0.1...uploads worked fine w/o the protoboard attached...attach protoboard and uploads stall every time...(I then tested the R2 version to find the same behavior).
I did a websearch about stuck uploading with the 2560 and read all the possible causes (the '!!!' issue, etc.). I played all the games with installing/deinstalling drivers, environments, etc. and no solution has worked for me.
Anybody have any insight into this issue? I am particularly baffled as to why attaching the protoboard makes the thing fail - I considered that perhaps a chip shorted internally causing something to be stuck on the i/o pin of the 2560, but cant conceive how this would affect uploading....

Any suggestion is greatly appreciated.
Thanks
J

  1. It is possible that some connection makes the upload fail when in the protoboard

  2. Can you test new WinAvr included in: http://arduino.cc/forum/index.php/topic,118440.0.html ?

I've had similar issues before. It came and went. The last time it happened I thought it had something to do with the serial comms to the Mega (after the USB to serial FTDI). As I have an IO expansion shield (not original) I checked and yes, its wire through to it. So I cut the TX0 and RX0 pins off the expander and voila, it works now every time first time.

Its probably related to a badly designed expansion board that led to noise being introduced...