In VeSys 2008 it should be possible to simulate most scenario's including complex logic, although it is important to remember that even though the simulation can be used to check functionality it is a "snap shot in time" and so there are some scenario's which would be difficult to replicate.
I have used VeSys to perform full vehicle simulations including complex ECU logic without any problems, for some simulation I have taken a simplistic approach rather than trying to create a fully representative model. For example with Fuel Injectors I simply had them all switch on when the engine was running (rather than firing sequentially) as my main test work was to validate the voltage drop was within our standards.
When you refer to loops and variables it sounds as though you are trying to do some complex simulation, the logic in VeSys was never intended to fully replicate that of the ECU. I have used VeSys 2.0 and it certainly has more scope for creating custom devices as opposed to the built in ones in VeSys Classic so it may have more ECU based functionality.
Maybe if you can explain a little more about the circuit you are trying to re-create there may be a way to achieve your goals in VeSys 2008.