Maya/custom hotkey preset problem

Ok, I’m editing this post because it was too long and I think it was scaring people away.

Since the maya interaction preset “fix” I’ve noticed some problems that weren’t here before. If you go into edit mode and select, for example, an edge, than perform an action like bevel, when you click to apply the bevel, whatever component is under the cursor gets selected.
I’ve tried messing with the inputs in the user preferences, while maintaining the same mouse buttons, but nothing seems to work - changing one thing breaks another.

Any help on this will be greatly appreciated.