What you're doing with turning on a video FX and mouse repeat for an AOE is designed to be done with a
Send Next Click Action instead of having to set up a Mapped Key to end it. The only difference is that with this type of Action it would use a cursor-based VFX rather than letting you use a predefined one.
But to answer the question as to why it is "bugged", you have a permanently enabled Mapped Key configured on Mouse1. This will disable and/or interfere with the normal behavior of Mouse1 as it relates to Inner Space and any of its GUI, like the ISBoxer Control Panel you're trying to interact with. Holding "Alt" (or another modifier) will prevent the Hotkeyed behavior, because Inner Space does not perform its Mouse1 hotkey when you press Alt+Mouse1. (That's why you can move it when you are holding Alt)
If you want it to be done the way you have it, do the following:
1. For the "end mouse repeater with left click" mapped key, go into Advanced and check "Do not load this Mapped Key when the Key Map is loaded". This will make it so the Mouse1 hotkey is NOT enabled by default
2. In Step 1 of "end mouse repeater with left click", add a
Mapped Key State Action to turn OFF the "end mouse repeater with left click" Mapped Key.
3. Go into "Pass 6", and in Step 1, add a
Mapped Key State Action to turn ON the "end mouse repeater with left click" Mapped Key.
This should give you the behavior you're intending. The hotkey will be disabled until needed (when you press 6) and then will disable itself again after you click.