I was auto-checked in for a flight tomorrow after an EUA and the boarding pass PDF that was e-mailed to me shows up with the proper number of miles. Reprinting mine from the web site I see zero miles. That fits with your theory. However, I just checked in my colleague. He is still on the upgrade standby list and has not been upgraded. His boarding pass, as displayed by CO.com shows zero miles, so this is clearly not related to having been upgraded. Tomorrow morning, after I check in for Saturday's flights, I'll have three other PNRs to report on.

Oh -- and by the way, there was no destination highlights rot on the two on-line boarding passes for tomorrow. Perhaps that's because it's for a return to my point of origin...