Nope, we're stumped. We have over 1,000 SkyView installs with the AP, and this is the first we've heard of this. I just flew SkyView with the AP a few days ago and it holds right on the altitude.
First things first, you have the bug up on the altitude tape, and you are saying that when the AP is level (and has been for a minute or more) that the bug is 40' away from the actual altitude?
The only other thing I can think of to check is your altitude adjust. Do you have an adjustment for the altimeter in the PFD setup menu? Just trying to figure out where the software bug is.