solved the problem, so i figured i should post in case anyone else is seeing the same thing.
it turns out, it has NOTHING to do with a second instance of emacs. i cant even open a SINGLE instance (i just had been running one instance since before i saw the problem i guess... only noticed this time because of a shutdown).
i changed the following and the problem disappeared. in my .emacs file:
(require 'cua)
(CUA-mode t)
TO
(load-file "cua.el") ;; or if you compiled it (load-file "cua.elc")
(CUA-mode t)
this did the trick for me... although i am not sure why.
thanks to all who commented.
PS - i am using emacs 21.3.1, so i do have an older version. if any readers have the option, justinhj's comment above (about upgrading) is probably the easiest answer. CUA is built into version 22 and above i believe.