Whoa, you may not need a new set. My question was that I ASSUME you are using a brand new set thereby necessitating this: pressing down on them as I said in the third paragraph. You must eliminate arc up over the saddles and nut.
Thanks and thanks to everyone who has responded. I tried a different set of flats and really didn't like them. So I took them off and put an old set of the LaBellas back on. The intonation problem has been worse at times. Despite evidence to the contrary on this thread, this web page, I don't think it's a string that is commonly used. I played upright primarily for long enough to develop a heavy touch though I'm learning to lighten up without sacrificing expression. Maybe that's not even why but I'm not comfortable with the 45 - 105s of any brand I've tried. So now I've got the old "Jamerson" Labellas (I don't know how old, it's likely a combination from old sets I've kept for spares) and the E string barrel is way back but there is still room and it needs to be more in tune. I believe it can be. The other strings are not a problem, though the action overall is a little too high.
After the show I'm playing is done I'll get a new set of strings and tackle the issue again. Two things were completely blowing my mind: a hot spot in the pit on E natural (naturally), very noticeable (at least to me); and whenever he bass is doubled the timpany it's not a tuner I want to consult, it's the Richter scale. The bass (a/o its player) can't be expected to solve either issue. Once I calmed down I mentioned this to the music director in private and he was encouraging. The next rehearsal was better. But my first reaction is it IS my problem. I was already vaguely dissatisfied with my set-up/intonation and I made this matter worse trying a quick fix. The LaBellas are not carried by any local shop which is my evidence that they are stings not commonly used. This is a (questionably) major city but since coming here I've been getting strings ad things on line and felt I didn't have the time to wait this time. Probably most bass players are wiser possibly less neurotic about these things, (though we all have our musical pet peeves I'm sure), and at the very least wouldn't overreact as I did.
But it's good to have a forum like this to talk about stuff with other bass players. Unlike horn players, electric bass players are pretty much one to a gig. We've got to to talk about our experiences on gigs and thoughts about instruments, strings, other gear, elsewhere. I suppose that's true of drummers and piano players as well. So I don't feel like a total fool for bringing up the issue. And all the responses here are now part of my Go-To library with things like favorite transcriptions, Fender's adjustment and care guide,a list of the frequencies relative to A-440 at each fret, my recurring dreams (there are a lot of them, I'm narcoleptic), pictures of my ex-girlfriends for inspiration indexed by type of emotion...Whoa! this all took a left turn, eh?