[BetterRed]

So what do you suggest might be the cause?

The OPs problem is Sigil V2 specific, i.e. his AHK V1 is operating normally with all other applications, just as it did with earlier versions of Sigil, just my AHK V1 does with Sigil V2 and every other application I run.

So where would the differences between the OPs setup and my setup be found… given its a Sigil-only problem the Sigil Preferences directory looks a logical place to start. When I look in there the most likely candidate I see is the plugins sub-directory… I also see the plugin preference settings are kept in a separate directory.

So, if I had the problem: I would close Sigil, secure its preference directory by archiving it into a .ZIP, delete the plugins subdirectory, and restart Sigil. If the problem remained I'd reinstate the reference directory from the .ZIP (then I'd try running in Safe mode to eliminate other tasks**). But if the problem disappeared, I'd reinstate the plugins one-by-one until the problem reappeared… and if it didn't I'd look for a brick wall.

** I have a problem imagining how/why a third task would consume keystroke sequences emanating from AHK V1 destined for Sigil V2 specifically… but only if AHK V1 was running with normal privileges.

BR