Can not switch windows

[LargeChicken]

I tried to search but the search function just ignored my search saying that every word in my search string was too common so forgive me if there's already a thread on this but I CBA to fuck with a retarded search function.
/rant

The problem I have is that, randomly, switching between clients (and sometimes anything on my computer) just stops working when I'm using Isboxer. What happens instead is that the window will flash orange on my task bar. If I try to manually switch to a window by clicking it on the task bar that window will pop up for a split second and then return to it's original layer. I've only ever noticed this happen when I'm using the hotkey (Ctrl-alt-{window number}) which initially breaks it and then the only way to fix it is to restart all my characters. It was a rare occurrence until today where it has started to happen within 5 minutes of starting my team. Is there a setting I can use to force windows to switch to the window I'm trying to switch to regardless of what's happening in the window it wants to be on the foreground? I know there is a setting like that within AutoHotkey (#WinActivateForce).

If there's no solution to this problem I may need to just outsource window switching to Autohotkey and disable the hotkeys within Isboxer.

Thanks.

EDIT: Not sure if this is a permanent fix but right after I made this post the glitch happened again and I was able to fix it by right clicking on the stack of game windows and then pressing a switch hotkey. Will report here if this fixes the problem every time it occurs.