I’ve worked on this guitar before, this time it’s come in to have a setup in preparation of a studio visit. The owner was finding it would intonate properly on the A string especially. At first I had the same issue and needed to get the string shorter that the saddle would allow, I though turning the saddle round might work but the spring was still in the way. I turned the whole bridge around and instantly had more normal result and it intonate perfectly, with the saddles sitting more in the middle of the bridge. The take off point of the string must have been off, I wonder if the the bridge was just on the wrong way round?
The nut had worn too low on a few strings, it being plastic it wasn’t ever going to last that long so I replaced it with a bone one.