Near as I can tell, the Gear Advisor … stopped working for me when I updated to 1.070… It did work in 1.068. This is a level 40 Night Elf Hunter, FWIW.
Settings -> !Gear Adviser Make sure the Loot Suggestion Priority is set to your spec and that it’s at the top. Place the mouse cursor above the spec name so the green up/down arrow appear and move the spec to the top by clicking the green arrow. If the spec isn’t shown then add it from the drop down menu below. Example: Beast Mastery Highest Vendor Price
Hrm. It had “DPS” and “Highest Vendor Price”, and apparently at least one of those were no longer valid, so it … just kept not doing it. Clearing the list and adding in BM and HVP again fixed it.