Syncing Profiles - Plugins??

Hi guys

I know I can simply copy the contents of my portable profile to my pc, and my pc profile to my portable (But I have to delete a portable.ini when I do this right??) but what I wanna check is if in doing so this will will it affect the plugins setup? I mean if I have plugins life quicktime which I think cant yet be made portbale, will it affect my portable profile ie cause it to leave behind registry entries?

Thanks for any help