ok, some things i've noticed:
If you go to the mouse control panel using the option inside the wrench menu (and doing so, a blue box with text appears to the right of the tray menu) , the tray menu can no longer be closed, Ctrl+Alt+Del to the rescue
Nosing around, touching the code (to add the hotkey), it seems that i've touched something, because the wrench, question mark, cross, scroll wheel, double click and mouse speed icons have been replaced with a "Ei" or a "Fi" text in bold (the point of the hotkey is to reduce the use of the tray menu, so no too much problem there, as it's also temporary).
Also, the help tooltips of the Double click speed and the Scroll wheel lines are displayed way up on the screen, it seems to be due to the taskbar (like if there is something avoiding a tooltip to be displayed over the taskbar, I've seen this behaviour on other AutoHotKey implementations).
On the other hand, now it works well in some windows that didn't like the swapped buttons! There is still this weird "SensorPanel" window of a program called AIDA64 that shows the values of some components of the pc, it has no borders, custom color, custom/customizable elements; there isn't a single mouse simulator/configurator/terminator/interpretor/modificator/etcetor able to use it in any other way besides the standard mouse. I don't really touch it (just configure it once and ready to be watched untouched, it seems), but it really calls my attention. It's my heavy artillery for this kind of software, but again, is more about trying to defeat that little window than anything else