One thing I recall about someone recently having issues with VMK-WIN is that the CTRL, ALT, SHIFT, and WIN are all activated on the falling edge of a pulse and don't go low again until another key is pulsed (whereas some other modifier keys behave as a toggle on rising edge). It helps to define the corresponding FB signals in SIMPL to make sure they're programmed correctly & FB isn't staying latched high.?
I also generally recommend right clicking the executable, going to Properties, and using the Compatibility tab to set it to run as Win XP SP2 (which is what it was written for according to manual).