I have a similar problem after the 1/1 patch. After finishing the Terran Lvl 30 bonus mission, my HU mission has advanced from step 8/17 (see MacKallen upon reaching Lvl 50...) to step 9/17 (Proceed to Yeagar Shipyards in Luna Sector...).
My Toon - Wells (TE, Lvl 35)
Thanks in advance :)