Ok, clearly some sort of app-level support is needed for some setups
Btw, as a workaround for a small part of this, you can give the go-through-a-wormhole order by selecting the ships you want to move, tabbing out to the galaxy map, and right clicking the destination planet. Not that this solves the overall problem, but I thought you might like to know that in general.
Chris, I'd take care of this but things have gotten highly insane over here in the last 24 hours. But I think I know how to provide the necessary workarounds for this, if you have time:
1) Making sure that all references to LeftCtrl/RightCtrl go through some kind of key-bind; the give-order-to-go-through-wormhole is a good place to start with. This may well already be the case.
2) Add a new AnyTime KeyBind that flips the Left and Right mouse buttons, like we did in Tidalis; probably default to KeyCode.None since this isn't something most players will desire, but some players will (apparently) absolutely require. Still seems strange that the OS isn't passing it in as a right click.