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No idea if this is related to your issue, but I was seeing something similar (also 14.04 and Mega2650). As it turns out, I had debugging turned on with a 3rd-party (i.e., non-ROS, non-arduino-supplied) object that was attempting to send data over the USB (as you know, on a Mega2650 board, no ethernet or bluetooth).

As was obvious to me once I realized what was happening, when another object fills the serial line with data, ROS won't be able to sync. Since your board does connect (at least sometimes), it can't be quite that easy; but, since your question was "Any ideas?", maybe the data line is being utilized by a non-ROS object?