Is the new board appearing as a /dev/IOIOx device? Are you using the exact same jar with both versions? What's the deal with the undefined IOIOLib version?
There have been some changes in the library that may have caused this problem, but I cannot see how the firmware version is related.
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There are maven targets for the libraries. Please refer to the wiki and or example apps. Can you please test the precompiled apps before proceeding to you own built ones?