Hi Dan
Official support for multiple Bpods in a single MATLAB instance is a priority, and will be released in the coming year (hopefully in the spring).
Support will necessitate a revised version of the Bpod object, containing the state machine assembler and all other code that currently interacts with the global variable BpodSystem. This encapsulation will enable us to ensure that operations of the separate rigs do not interfere with each other at the level of calls to the file system, or calls to the hardware. Unfortunately, this update will necessitate a revised syntax for behavior protocols.
e.g. TrialEvents = StateMachine1.runStateMachine() instead of TrialEvents = RunStateMachine()
It's hard to guess what's causing your current issue, especially since it isn't present on your second set of (otherwise identical) machines.
One possible culprit for dropped data is a faulty USB cable, and/or its mating USB connector on the Arduino board. That being said, if you do not see the issue when you run either of the Bpods individually, it's likely something else.
Is it one of the Bpods of the pair that always crashes? Or is it either at random?
If you swap the Bpod and/or USB cables with the machines on your second computer, does the problem move with it?
-Josh