From what I can tell, the problem is that you are using a modifier in the main key bind -- "Shift+1"

What's happening when C is the lead, you press "Shift+1", then when it gets sent, a, b, & d are actually receiving "Shift+Alt+Ctrl+Semicolon".

This took me forever to figure out as I had the same problem which is that if you don't use "Pass only hotstrings", the keypress of "1" would actually trigger it and pass whichever modifiers are held at the time to the clones. I can't recall why I couldn't use "Pass only hotstrings", but I know that was giving me more grief than not, so I finally changed all my FTL keys to be unmodded keys then everything works as expected.