Yeah this was a bug that was introduced with LOR. I filed a report about it, twice.
If a key combination includes a modifier key (like CTRL), and there is no bind defined for that key combination, the game will process any binds that happen to be defined for the key without the modifier. <CTRL-1> becomes <1> and so forth.
The way to stop it from happening is to create a null bind for the combination with a pair of empty double-quotes: /bind control+1 ""
I have a Logitech G19 and was thinking about binding my key skills to quick fire keys. One thing that you could check (or double check) is to make sure you have the right drivers for your keyboard. If you don't it may not work right with STO as, I know with Logitech they have specific profiles for specific games.
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Rather than single key, use a key sequence to put a 0.02-sec delay between ctrl/shift/alt's downpress and the number key's downpress and another 0.02-sec delay after the number key's release and the ctrl/shift/alt key's release. This ensures both keypresses register in the game in sequence.