I think http://www.gamesas.com/index.php?/topic/1172784-problem-with-magicka-based-spell-advancement/page__p__17326331__fromsearch__1#entry17326331 is one you were looking for.
The one I was trying to find was actually a thread that started right off with a solution from the first post. The person put up a solution and then said it should work for other magicka progression mods different from the one he was using. At this point I'm thinking I must have dreamed it or something.
In any case, going off what was posted in your thread, I looked at the Improved Skilled Magicka script with EE and found this:
; Check if player is in magic mode, if not, exit the script
if ( player -> GetSpellReadied == 0 )
return
endif
If this is the part of the script that needs to be fixed, I have no idea how to proceed. Again, knowing nothing of scripts.