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We might have got this one resolved. We currently use an endpoint security product, (application whitelisting), called Palo Alto TRAPS. It is not anti-virus per se, nor does it actively scan files/folders/shares, however, it does perform process inspection. We tried excluding the C:\Program Files\Immidio\Flex Profiles\* folder and so far, the issue has disappeared.
The TRAPS logs indicate the FlexEngine executables are being allowed to run, no errors discovered, but it seems just examining the FlexEngine executables as they run seems to cause a problem.
So, fixed for now. Thanks all. Hopefully this thread is useful for someone else.