Question: Valentine Trem – tuning stability

I have recently acquired a 2017 Valentine trem – Buttermilk. It came strung with 11’s but they are too heavy for me so I changed to 9’s. I have set the trem springs so the trem is flush with the body (no floating), set intonation and added a tiny bit of relief to the neck as I’m a fairly hard player, oh and thoroughly stretched the strings and added a little nut sauce. It has now been set up with 9’s for three day’s. The main tuning problem is with the E and A strings. If I tune to pitch using either the Kemper or Boss tuner and then play (for example) an E or A chord the tuning is way out. To get the tuning correct I have to have the E tuned -10 and the A -7. Sounds really odd but that’s the only way you can play any chords in tune. Has anyone else had anything like this before.