If both are on (Repeater and Keymaps), then Keymaps have priority.

If Repeater is enabled in one window, and then you switch your active Slot, that messes with Repeater.
Basically, you want the other windows to be copying the active window, so this is intended behavior.

I'd check to ensure the Keymaps On/Off toggle, is toggling any new Keymaps you have made.
If you are making Mapped Keys, and they're in an existing Keymap (General, FTL DPS, Control), then the toggle to enable/disable Keymaps will work fine.
If you've made your own Keymap (a collection of mapped keys), ensure the Control Toggle enables and disables the new Keymap too.

If you cannot figure it out.
Click on File, and copy your profile to clip board.
Ensure you are hiding your account info.
Go to www.pastebin.com and paste your profile there.
Then paste the link here.
Or better on the forums at www.isboxer.com
Lax is really good at troubleshooting specifics.