It's possible that it's occurring too fast like that for STO. What's happening behind the scenes is that Alt + 3 is pressed down, then the pause, then release 3 and then alt (there is no pause between alt and 3). This works ok for most things, but STO may have a different way of polling.
Press down Alt
Press down 3
Pause .05 <--- may not be necessary
Did STO have an update? VA hasn't had an update in that area of code for a really long time.
Hope that helps!