Apparently its not a problem with the modifiers themselves, but something to do with my mouse. If I actually use the Ctrl or Shift keys it works fine, its only when I use mouse buttons bound to Ctrl or Shift that it doesn't work (using a mouse button programmed to Alt works fine). Strange thing is that the mouse button modifiers work just fine for casting abilities unless I'm trying to use the focus modifier too.
Edit:
It seems ToR isn't even fully recognizing the keystroke commands from the mouse. I swapped which mouse buttons were set as Ctrl and Alt on my mouse and the game behaved as if they weren't changed, even after restarting the client. It must be recognizing them as M4, M5 etc rather than the actual keystroke. But when I program key bindings in ToR I use the mouse buttons to do so and it registers as a keystroke for that.