Motormouth, I would recommend you post on the eab thread. A bunch of people have had similar issues to what you're seeing, most of which have been resolved.
Have you tried a fresh workbench install? It is recommended to start with no more than wb3.9 + bb1 and bb2 to try and rule out a dodgy patch causing issues.
Have you tried tweaking the setcmemdiv parameter? Sometimes allowing the sonnet to autodetect the cachemem speed causes instability.
SetCMemDiv (0-5): Sets the speed divider of the L2 Cache memory. 5 = 3, 4 = 2.5, 3 = 2, 2 = 1.5, 1 = 1, 0 = Handled by library. Default = 0. For example: A Sonnet with speed 500 MHz and setting 5 will run the L2 cache at 166 MHz (500/3).