Hmmm,
I think this may be happening after the departure runway is selected in the FMS. Its rotating the map in the direction of the runway to draw the runway but not rotating back to draw the route.
Unfortunately there's no way to un-select a runway from the FMS without loading a new flight plan. So it stays stuck in that rotated position.
For now try this hotfix install, and see if that works for you.
http://www.isgsim.com/dl/ISG_151_HotFix.exe
Note: this hotfix will only work if you already have the full version installed.
Regards.
Ernie.