In my case, when I start the program...

I need to press M3 (hotkey to enable Keymaps).
This turns the M3 light on and enables Keymaps.
I then press M3, which turns the light off and disables Keymaps.

I then press M1, which turns that light on and enables Keyboard Repeater.

By doing that, I can enter my passwords and authenticator code in each window at once.

You could try pressing whatever hotkey you have for Keymaps to be sure they're off.
Even if you turn them on and then off.
Do the same for repeater (or keyboard repeater, if you split keyboard and mouse repeating to different keys).
Then you can type normally without issue.

Basically, in Keyclone you need to press Pause to type without a problem. I'd imagine most of the boxing programs will have something you need to disable to type freely (ie not broadcast anything).
With IS Boxer, repeater is probably off unless you turned it on.
However Keymaps are repeater options for specific keys only.
If these keys interfere with what you're typing, you need to disable keymaps to type freely.