I have a suggestion for you.
I had a similar issue to you, when I switched windows either via keyboard or mouse the key repeat turned on (but not mouse).
I redid the layout wizard and noticed Lax doesn't have the wizard set to use a key to switch windows.
So I set my slots to not have a key to switch, fired it back up and lo and behold when I switch windows (just by mouse), no repeat.
For kicks I then took it all down, loaded up a default config from the wizard, added a key invocation to the windows, and switching does NOT enable repeat, so there was some interaction in my setup.
And then I loaded back my own config, added back in the switch keys, and now it doesn't repeat. So, I don't know what the issue was, I can't reproduce it, but try unsetting and reseting your window switch keys, or if all else fails - try exactly what I did above (about clearing and making a new default config, loading it into innerspace, then switching back to yours and adding the window select keys).
If someone wants to review my profile here you go.
No window select keys
http://pastebin.com/m1f6a6520
With window select keys
http://pastebin.com/d50b394e2
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