When you train new ranks of spells, the spells on your toolbar are automatically updated to the new rank. They are not, however, updated in any other place. In Merlot's case, the secondary spec toolbar used for healing, which is set up differently to the primary toolbar, was not updated with new ranks and Merlot was unintentionally using downranked spells for healing.
After reading the post about it, I went home and checked the spells I had set up with Clique, which I am using to mouse-click-bind my healing spells. I'll go into how Clique works another time, but I discovered I have been healing dungeons using Healing Touch and Rejuvenation rank 9 when I had rank 12 available, and Regrowth rank 8 when I had rank 10 available... /blush.
I haven't tested it with any other addons, but I would recommend checking not only your secondary spec bars, but also your stance bars (eg. the bar that appears after you change into a tree), your settings for Healbot if you're using it, and any other addons that are assigned spells.
I also have not tested this, but I am 99% sure that macros are not affected by the rank bug. Spells in macros, unless you specify a rank to use, will just use the highest rank available.
Now I just need to write a note to myself to re-do bindings at level 80 before I try to heal anything heroic!
