Semi - tuning problems

[Leon Transaxle]

Can anyone explain to me what's going on here?
I have a jazz box type semi acoustic with a floating bridge.
When I first got it I couldn't get it to intonate properly with whatever cheap strings it came with.
I fitted it with flatwound 11s and it was fine.
The strings are now about four years old so I thought I would replace them with something roundwound and a little lighter. I also replaced the tunamatic type bridge with an all wood, compensated one.
I fitted D'Adario 9.5s. Now, once again, it won't intonate properly. Tuned with a Snark most open chords are OK-ish but an A sounds horrible, particularly on the D string.
The bridge is correctly positioned. Top and bottom E intonation with 12 fret note and harmonic is spot on. The other strings are barely out considering the limitation of the bridge. The D is certainly no worse than the others.
On restringing with the old 11s its fine again.
What do I do with regards to new strings? Is it a tension thing? Will another set of 11s work? Will roundwound 11s work?
I'd rather not work my way through the local guitar shop to find out. There is mellow and there is sounding like a dead fish!

[BigRedX]

Nut cut too high?

[Leon Transaxle]

Genuine question not a challenge - How does that create intonation issues? Just from the maths/physics the difference in string length would be minuscule and wouldn't appear to change with gauge. Musically/harmonically I don't have the experience to know.
If anything I would have imagined too low a nut would have an effect in that a thinner string would sink to the bottom of the nut whereas a thicker one could get 'stuck' part way down.

Like I said not a challenge, just an inquiring mind trying to comprehend the reason behind things.

[Ancient Mariner]

It's the player, rather than guitar.

You're almost certainly fretting too hard and bending the strings sharp, and the duff A chord is a major clue. I can't use anything less than 10s most of the time for this reason. When true jumbo frets first appeared it caused lots of problems/complaints when the higher than usual frets allowed strings to get bent sharp. I had a mate who bought a new Ibby Artist with these incredibly tall frets (for the time) and it was a real problem because we all used 8.0 gauge in those days and they'd bend if you breathed on them..

[3below]

Jazz box, shorter scale 24.5" ? As above I would suggest heavier strings, 10s or 11s. I tend to use 12 or 13s on mine. Like you I also had problems getting mine to intonate correctly. Eventually I took it to my local luthier and it came back perfect and has stayed that way since. This was one guitar (or bass) that defeated me on setup (he also sorted my G&L bass that also defeated me). Sometimes there are complex issues that we mere mortals can not solve, however the evidence above suggests big strings. Make that guitar top work hard

Edited October 6, 2013 by 3below

[Leon Transaxle]

Thanks guys.
Player issues sounds a pretty good explanation. I do arch my finger to fret all three strings with the one finger but having short fat fingers means there probably is a fair amount of lateral force - just never noticed it before on my electrics which are strung with 10s.

To be honest I haven't noticed whether there is a difference in scale length to my other guitars (but it's quite likely as they are a Yamaha strat-a-like and a Variax)- I shall have to get the tape measure out now.

Sounds like it might be a combination of the the above.

I found some bargain flat wounds 12s on the Dawsons web site on Friday and have fitted those. Intonation is fine now. The action could do with a bit of work and I need to develop cat-like pads on my fingers, but hopefully I'm sorted.
If I want to wimp out on lighter strings I'll play something else!