Originally Posted by Dante_Stella
It's probably changing the alignment of your eye to the RF, which does cause back and front focusing. Maybe your RF was actually off but appeared to be correct by virtue of your eye position without the mag.
Ah yes, I am aware of this effect... I've noticed it affects vertical alignment too.
After some testing, I think I've confirmed that you're right about the eye alignment part. The magnifier causes a significant 'tunnel vision' and my tendency is to subconsciously center the frame lines in the visible window. This puts my eye closer to the left side of the eye cup at the distances I was testing at. If I very consciously 'center' my eye on the eye cup, the frame lines are not centered in the visible window, instead they are closer to the bottom right corner. But shooting like this, the backfocus is gone.
Because the 90 frame lines takes up so much less of the frame without the magnifier, I don't tend to do this without the magnifier.
Thanks! Mystery solved. I can now happily continue to use the magnifier and still get sharp focus.