Detroit,
It's all about the tension between the strings and the springs, in a F.R, all the strings are connected, so to speak. So when you tune it one string, the others will be affected.
You'd have to tune it repeatedly. Tune from the lowest E to the highest, and repeat this procedure. The tunings will always be slightly off, until all the strings are in 'equilibrium', or stable. Apologies for the bad explanations.
Anyhow, it will eventually be all in tune, just keep tuning, and tuning. It takes a while.
I hope it helps, it works for me.
Correct me if I'm wrong.
:lol: