I asked because I got a slight difference in the other direction when I bare shaft tuned. Bare shaft tuning indicated that I should have a higher nocking point for 3 under than for split fingers, in all cases. For most bows, I noticed no difference in spine. For one bow, where the nock point was already pretty high for split fingers, I had to move it up to 7/8" before I was able to get good arrow flight shooting 3 under. For that bow, moving the nocking point up to 7/8" made the bare shaft that had shot fine at a lower nocking point for split fingers indicate that it was too stiff. I was never happy shooting that bow 3 under, although it shot fine split fingers, and I eventually sold it.
Now why would you get an opposite indication? I can think of no mechanical reason having to do with the bow or arrow. Do you think there could be a change in your draw length or release that could cause you to need a stiffer arrow? When I attended Rick Welch's class, he changed my anchor at the same time I changed to 3 under, which resulted in almost an inch increase in my draw length, which would of course increase the effective poundage of the bow. Later, when I attended Rod Jenkin's class, I started using a more dynamic release, which increased arrow speed some and could also result in the need for a stiffer spined arrow.