I am using the latest update of Keyman, just updated it, and I am using a keyboard that I created.
Upon further investigation, it actually seems that this issue is actually isolated to OneNote. I hadnˈt noticed the issue was isolated to OneNote since I hadnˈt been using the keyboard in any other program and actually trying to copy/paste/undo. But now I have tried the same keyboard in other programs with no other issue using regular keyboard commands. And yes, I did go back to OneNote after having success in the other programs, and the issue persists.
Previously Keyman just didnˈt work at all in OneNote but a recent update (I think it was actually a Windows update) made it so that it does work now, only it seems to have developed this new problem after resolving the old one.