That was a pretty annoying bug. I never did find out what the problem was as I moved onto other problems and chalked that error up to some undiagnosed weirdness on that particular server. From time to time I would get asked on Twitter if I had ever solved the problem. My answer was always "no, and if you do solve it please let met know how you fixed it." Today, my friends, was the day.
Based on a response from Demian Katz, he was able to get around the issue with flag set on the PHPUnit command line - "-dzend.enable_gc=0". Apparently the issue has to do with garbage collection and has been a known issue since the beginning of 2011.