In the month we had the glyphs before WotLK (haven't played my mage since the release), that happened to me twice in an instance. Just out of the blue it started applying only one debuff percast. At first I thought it was due to the boss we were fighting, but this bug continued for the rest of the instance. Relogging fixed it for me.
Something you can try in addition to verifying you are talented for imp. scorch, you can just buy a new scorch glyph and reapply it. They are cheap and the "reinstall" is always a good default "fix".