I use the 2-way linear spirit levels on my
Manfrotto 029 tripod head (not sure what Bogen number that is). I find it easier to level than the bubble-type ones. I use a Manfrotto L-plate (often used with the QTVR heads) , and before shooting, calibrate it for vertical use with a
Hama 2 way hotshoe level
Before using the head, I calibrated my levels using a builder's level (one of those ones which are supposed to be accurate to 2cm in a kilometre, or something like that). The levels can be finely adjusted using a hex key in the grub screws. I then plugged the grub screw holes with blu-tak to avoid any unwanted fiddling. I check the accuracy randomly to make sure it's still in, as my tripod can take a beating.
When I calibrated, I made sure to do it on a concrete floor, to avoid unwanted vibrations.
I find that most problems are indeed caused by out-of-plumb walls etc, or just by encroaching barrel distortion.