I should have explained that better. The tuner seems to think it's doing it's job properly - I tune the string down and it shows it to be "correctly" on the low D, etc. But then when I'm finished with the other strings and try to play an open G chord, it's clearly not right. I haven't mapped out exactly which strings are off and by how much (and of course a few don't change from standard tuning). It may just be that the low and high D's are off, but it tunes the other strings/notes correctly, like it always does in full standard tuning.

I'll try using a different pickup selection and/or where I pluck the string. Just seems odd that it only does this when I try to change to Open G.