keyboard - Autohotkey bug. Workaround?

In windows 10, I switch between a Greek Polytonic keyboard and a normal English QWERTY keyboard. I have an autohotkey script which swaps the left control key with capslock.

settitlematchmode, 2
#IfWinNotExist, ahkblock
capslock::lctrl
lctrl::capslock
#IfWinActive

However when I switch to the polytonic greek keyboard, for some strange reason autohotkey interprets my script to mean that I want the right alt button to function as a second caps lock key. This is unacceptable because I need to use that right alt button in order to combine iota subscripts with breathings and accents.

Do you know of any workaround or bug fix for this issue?

Answer

I ended up using an alternate method to swap control and capslock (I found a program that lets you change the key mappings in the registry directly - sharpkeys), and now I use Autohotkey to swap them back on the rare occasions that I need control to be in the bottom corner of the keyboard.

My autohotkey script now reads as follows:

settitlematchmode, 2
#IfWinExist, swapcaps
capslock::lctrl
lctrl::capslock
#IfWinActive

So if I need to temporarily swap the keys back to the standard layout, I just need to open a cmd window and set it's title to "swapcaps"

This isn't an actual fix for the bug, however it is a workaround and it works just fine. (Arguably even better than the original autohotkey solution, which was not flawless)