If you have the new version, just hit the scan button and it should fix everything. It shouldn't be a problem if you have it in different locations, but 2 different versions can be a problem.
Edit: Oh yes. 1.09 recalculated the port arbiter but didn't save the new value.



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The only thing that's really changed besides the auto devcon thing is probably the delay in opening the serial port after resuming. It's about 8 seconds right now, and was 20 in earlier versions. I wouldn't expect that to be a problem though.

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