Were you still logged in when you downloaded 1.3 and tried it out? If so, you might want to do a /reload or if you already exited the game, login and try it afterwards. You have to do a /reload most of the time when a profile is Updated and PQR is never closed.
Anyways, I logged in just to see if anything is wrong and it all works for me. All addon's shutoff, still works. All my main addon's on, it still works.
To help me figure out what the problem is, disable all addon's then load up PQR. remove all abilities from the rotation except -- Load Lua -- and then add 1 back at a time and see if that 1 ability is firing. If it is, move onto the next and so on till you try out all abilities and find the one that is messing up.
If you do not want to do this, there is nothing I can do to help you as you will not help me find the problem. Enough said.
P.S> I tried it with both of those glyph equipped and it worked as well as tried it without both of them and it still worked. Maybe its another glyph that changes spellID? I don't know. What glyph are you using?