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Double Bass Bow/Pizz Intonation differences

I have always played passages with the bow to a tuner, then pizz also to the tuner. A month ago, my open strings while played pizz were in tune, but the tuner displayed (and my ear) that the pitch when bowed was flat. The difference is worst on the A and E strings mostly in Half and First position. Could this be a set-up issue? I've been experimenting with string height. Has anyone experienced this or know of a remedy?
 
Pitch varies when a string is bowed, depending on bow speed and pressure. When setting intonation on C extensions, I end up setting to an average because the pitch keeps wavering. If I use medium pressure and an even bow stroke I can get it pretty constant, but not perfect.
 
Also, when a string is plucked, the tone starts out higher and then goes flat; maybe that would account for what your tuner is picking up vs. arco. Think of say, a floppy, tuned down guitar string plucked hard; you get the "bwowww" tone. I think that's why so much of the down-tuned rock guitar sounds out of tune and noisy.