If there’s one thing I’ve learned from using AutoHotkey it’s that there are several ways to send keyboard events to Windows, and not just one standard way. It’s more complex than “send it this standard way” and expect it to work with everything.
I’m inclined to say this is a bug in MultiKeyboard Macros that needs to be fixed rather than a problem with any particular target application. It’s up to MediaChance to fix any issues MKM is having with other software, not incumbent on the target software to change something to be compatible with MKM. After all both Chrome and Anki are working as designed and between them have millions of users.