Ian,
You've spotted the fatal flaw in our current policy
If you're using the current FLogger, you're going to get the FS times not the local times, and there's nothing we can do to stop that in the current FLogger...
Next FLogger (v4) we could perhaps ensure "correct" hours are logged, but I wouldn't like to say for certain (Andrei is developing the client, not I)
As for ProPilot, the rules for PP state categorically no acceleration whatsoever.
As for the online networks, I know IVAO operate a 20 minute policy. I've only ever been contacted while long hauling once (a polite /msg from a SUP to check the plane was manned, sort of thing) but better safe than sorry; if you intend being away from the cockpit for anything more than 5 minutes, don't fly online at all (or if already online, disconnect).