Processor affinity screwed up?

IMHO The easiest solution would be to write an app_info.xml for the 6.04 App that uses the file einstein_S5R4_6.04_windows_intelx86_1.exe as (only) App binary, thus avoiding the switcher process. You'd need to update your App manually then, but apparently you're used to tweaking your BOINC installation anyway.

BM