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I tune my bass slightly flat when recording. Is that wrong?

OP is talking about a fender jazz not a high end dingwall. was not really replying to you just the general comments that a pro set up will make that jazz perfectly in tune. it will not.
You two are basically talking about two different realities. There's a big difference between being 100% or 'perfectly' in tune for every note all over the neck when metered, and being out of tune enough that you have to compensate by tuning the bass at the 5th fret so that you can play with others without sounding out of tune. The former describes the reality of tempered tuning and fret layout, nut cut, etc, the later describes a problem with set up that can be fixed to 100% as far as the average human ear is concerned-even if the tuner says you are slightly out. keep in mind- an electronic tuner tells you you are slightly out of tune, long before the average person- even a musician, can really sense it. The OP very much notices being out of tune to the point he has to compensate with his tuning- this means he is way out of spec somewhere on the bass- most likely nut too high and string length wrong (intonation).
 
For the record, I was able to bring the intonation to a reasonably good level. It's still not perfect due to the banana neck this vintage instrument has developed over the years, but it's not so bad now.

In the time that I couldn't take care of the intonation issues, I was able to go through the recordings with the slightly flat tuning and laid down pitch perfect tracks.

Somebody mentioned using Melodyne... I did that too and was amazed at how well it worked. Virtually no sign of tone degradation. I realize it might be a good habit running important bass tracks through it anyway, just to be sure...

Thanks everybody for the input.