One factor that's involved in guessing the IV's of a Pokemon is whether or not you have powered it up. This is apparently due to the fact that it takes two power-ups to raise your Pokemon one level, but wild Pokemon never half a "half" level.
Just looking at my list, I don't always remember if I have leveled some of my Pokemon up yet. While the difference doesn't appear to be significant, it would be useful to know.
Is there any indicator in the UI that you have powered up a given Pokemon before? (I checked the journal and didn't see anything there).