Ya I'm going to make sure my equipment is properly calibrated and use a glass thermometer I purchased from my LHBS. I'm also going to try a small 2-3Gallon BIAB and see what sort of efficiency I get.
I would try using the same process or only changing one variable at a time to insure you find the source of your problem. Decreasing batch size and going to BIAB might make an increase (or decrease) in efficiency, but you will not know precisely why. Calibrate your new thermometer and brew a new batch using the same process as before. Use a little more grain and plan for lower efficiency if you want the recipe to still turn out as intended or compensate with DME at the end of the boil.
Incorrect volume measurements can also impact efficiency (ie. using too much strike water and /or sparge water compared to what the recipe calls for). This is easy to check for and I'd check for it, both pre-boil and post-boil.