I ran into the same problem when I used SW 2009, can't remember which SP. It went away when I upgraded to my current version, SW2011, SP0, x64. Perhaps you could try a different SP.
Hope this helps,
Problem has been reproduced by SolidWorks.
They are trying to determine the root cause.
The FloWorks developers in Russia have found a work around for now....
Running as administrator seems to solve the problem.