I can't say I've experienced/noticed this. Are you taking the magnetic variation between true north and magnetic north into account?
As for the ILS, some runways actual courses are a bit different than their names suggest. For example
KORD (<--pdf link) runway 4R's course is 44.3 degrees, not 40.
I'm not sure why an ILS would guide you in parallel to a runway unless the runway course is entered into the autopilot incorrectly or the scenery doesn't match up right.
If none of the above is the case, could you list the add-ons you're using and/or some more specific examples(airports, runways, planes)?
I hope this helped.