The first thing to do is to stop using a repeating when in your events. Key-Pressed doesn't work well with events using when if any repeatition is required. Switch over to using every-time instead.
Second don't use the 1-4 keys. I know that they seem like the logical choice since nothing uses them in single player but you're asking for trouble if you use them in a repeating event too. I've had some limited success if I instead use one of the keys that actually has a current (but little used) purpose. B works pretty will in a mission with no bombers for instance.
There are some other pitfalls but at the moment mantis is taking an enormously long amount of time to load for me and I can't get to my original bug report to jog my memory. That should hopefully be enough to be getting on with for now.
EDIT : As soon as I post Mantis suddenly spits out all my bug reports

. Here's the
original thread I made when researching the problem. Unfortunately it looks like all the pictures are gone now.