Just my $0.02:
Try using a Peterson Virtual-Strobe tuner. That thing has such resolution, EVERYTHING is slightly sharp or flat, LOL!
Personally, after seeing and hearing the difference, I would NEVER set intonation without a Strobe or Strobe-type tuner. That ridiculous accuracy is head-and-shoulders above ANY digital non-strobe-type tuner. My guitar guy uses a very old (but perfectly functional) Conn Strobotuner and you can HEAR the difference.
BTW, adding to the above. ALLWAYS adjust and ck your axe in the playing position, NOT on it's back...Truss rod(s), action, intonation, etc. Otherwise, it will be off.