I found out the problem, I had an old app that I had installed many years ago and forgotten about, that was causing trouble, called "MagicPrefs". I had only partly uninstalled it so it was functioning in some way through a custom preference pane that was not uninstalled. After uninstalling all files associated with MagicPrefs I can now assign a mouse modifier to Ctrl+CMD+LClick in Reaper and the "move window" behaviour is gone.
Thanks o_e for your help! Knowing that you could not reproduce the problem made me suspect it was coming from some kind app extension rather then the Mac preferences.
I hope I can help you back someday!
Thanks!
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