andy474x
Knows the Drill
Strings binding in the nut is the most common cause of intonation issues on SE's - they are often filed for a certain string gauge (often 9's, but I'm not sure what is coming on the new 594's), but if you've gone up a size, or it's simply a very tight slot, that's probably your culprit.
It's an easy fix for any local tech to file the slots a little bit, and if you like the guitar, I wouldn't send it back until you have that looked at. Once the nut has been addressed, I've never had an SE that wouldn't stay in tune, even with stock tuners.
An easy way to tell is to bend the string on one side of the nut, check the intonation, then bend on the other side of the nut and check intonation again. If the intonation is going back and forth (sharp and flat), it's the nut.
It's an easy fix for any local tech to file the slots a little bit, and if you like the guitar, I wouldn't send it back until you have that looked at. Once the nut has been addressed, I've never had an SE that wouldn't stay in tune, even with stock tuners.
An easy way to tell is to bend the string on one side of the nut, check the intonation, then bend on the other side of the nut and check intonation again. If the intonation is going back and forth (sharp and flat), it's the nut.