Hm. Due to my experiences - lasting more than 3 years - with my 513 I state she is ever in tune.
But my custom made guitar had severe tuning problems. Everything was set up perfect by the luthier. The angle of the headstock, the bone nut, the set up of the tremolo (with a blackbox as countermeasuring device for not going out of tune).
Even strumming the guitar without tremoloing lead to untune the guitar in nuances.
First I changed from Sperzel Trimlocks to Phase III. Than I put more tension on the springs. Third I changed string gauge from 009 to 010.
I started getting better but not with perfect result.
I decided to call a guitar tech in my neighbour hood. And beside his own business he does professional reviewing of guitars for German Gitarre & Bass magazine.
I descriped the problem.
And he ripped off the blackbox out of the spring compartment, put in a third spring, than he rasped the nut. And than he puts his full attention on the tremolo (Fishman VS-50P, same as Wilkinson VS-100, but with piezo).
He inspected the guitar and found out, that the strings go over 90° edges from the block to the slide (where the piezos are integrated). Especially the the wrapped strings got stuck in there while tremoloing which lead made the made out of tune.
He rasped all the edges to made the strings go around very smooth corners.
After his work the vibrato works well and the guitar has got it´s supposed very stable tuning.
He compared the Fishman VS-50P with Wilkinson VS-100. The VS-100 has very smooth edges, but not my VS-50P.
Maybe - whatever cause - you have the same problem.
Is it a problem from the beginning or is it new? Did you change anything?