Are you hitting Shift+Alt+R at any point?

Part of your configuration might be confusing you. Shift+Alt+R is going to toggle both Key and Mouse repeat from the current window (not applying this change to All Windows). Then your Repeater profile has Key Repeat on by default, and toggles for Key Repeat and Mouse Repeat on All Windows. So if you start out by hitting Shift+Alt+R you're disabling Key Repeat and enabling Mouse Repeat on your current window, then hitting Mouse4 will toggle Mouse Repeat on all windows, making it off from your current window but on from other windows. So switching windows could give the appearance of "hey it magically turned Repeater on, wtf!"

Beyond that, no way is it toggling Repeat when you switch windows. Hope this helps you track down how you're getting it confused either way