Well, that nasty PAUSE problem can be annoying. Therefore there is a simple trick:
Load the game, prepare your aircraft, fill in cargo and fuel, start multiplayer software if you want, and start the Logger only when you are ready for pushback ! Also, you do not need to place your plane to starting spot by the Logger. Just select aircraft and flight, and that is enough

This way you will not lose paused time, and you will not mix the things in FS

I do not know your specs, but you can see my at the bottom...I think my PC is a quite old machine, but runs fine all the programs at once you mentioned:
- FS2004 fully packed with scenery and AI
- FS Navigator
- FS Screenshot
(- FS passengers) sometimes
- ActiveSky weather
- Adobe Reader for browsing charts
- FlightLogger
- browser for EHM ProPilot portal
- browser for surfing...
- Messenger
and occasionally the multiplayer overload:
- IVaP
- IvaE
- TeamSpeak
sounds terrific much, but works fine

... and sometimes I am even watching movies when get bored
