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This is probably because the program items are advertised. I have 2.7 and 3.3 installed, and when I pin the 3.3 Idle it switches to the 2.7 one. I guess there's a GUID somewhere that makes the two icons identical, but I don't know where that would be. This probably causes the icon cache issue (which I also see with 3.3.1->3.3.2).
The 3.5 installer will not use advertised shortcuts, so they'll be direct links to the exact version of the launch script. This should cut out a whole range of conflicts between different installs.
In any case, suggesting a reboot just for an icon is not a great look. It's bad enough that we require admin privileges for a per-user install (also on my list...). Hopefully the change to non-advertised shortcuts will fix it, but otherwise it probably doesn't need more than a note on the last page of the installer (which nobody ever reads, but short of forcing unnecessary reboots there's not much we can do about that).