Well the "foobar" fix previously was to pass through messages when normally they would get blocked - it only happens when switching away from foobar with a mouse click (and if you have the default "allow profile change on mouse move/hover" active then its unlikely to have made much difference. However, its quite possible that the requirement for that fix has gone away (it was introduced many years ago and I'm sure foobar has moved on since then, for sure XMBC has!)
Is it better, worse or no different at all?
I suspect foobar itself has a mouse hook, and I think there may be a conflict but given it only seems to happen when foobar is installed and running, I doubt there is very much I can do about it.
Its caused by windows getting too many or too few clicks such that the down and up get out of sequence, and then Windows thinks the mouse button is held down - and the only way to "fix it" is to reset the windows input buffer - CTRL+ALT+DEL usually does this but maybe you need to click in the CTRL+ALT+DEL screen (not on anything) - thats always worked for me - and I get it quite a lot when debugging XMBC).
Unfortunately, unless I can isolate a specific issue in XMBC, there isn't much else I can do

If there is any particular thing that break it consistently be sure to let me know (I have foorbar installed on my desktop now too so I will try and keep it running to see if I can reproduce the problem). If its only an issue with portable XMBC that would be interesting.. I generally *don't* run portable mode and portable mode is not a lot of use for me because I have such a mix of admin and normal apps (not least my dev environment) so I need the installed one so it works everywhere.