Hi,
That is a strange interaction. I would have thought you would be able to avoid that with removing the IMC and then adding it again. Are you adding and removing the IMC in quick succession, or are you removing it once you open your popup, then re-adding it at a later time when the popup is closed? I would be inclined to trying the latter if you aren’t already. It might also be worthwhile playing around with the options available for adding and removing IMCs, i.e. in particular the Ignore All Pressed Keys Until Release option to see if setting it one way or the other improves the behaviour you see.
One other thought is are you able to remove the reliance on setting input modes by solely dealing with adding or removing IMCs? I could see that as another way forward.
Lastly, and this is less of a solution and more of a general recommendation, I would encourage you to look into Common UI if you haven’t already. It solves a lot of these input routing and layered UI issues, and it works a lot more seamlessly with Enhanced Input.
Thanks,
Hayden