I think it is the well known bug that prevents miles being posted if you upgraded using miles. If it is, goodness knows why this still has not been fixed - it has certainly been there since April 2007 which is the one and only time I have ever used miles to upgrade on a LHR-EWR flight.
Was a right pain I recall to get them properly credited too
You are mixing two issues here.
a) Upgrade with miles, you should receive the miles & TPs for the original cabin you paid for.
b) Upgrade with cash, you should receive the miles & TPs for the upgraded cabin you have paid for.
I think the problem with being awarded no miles at all is more common with a).
The more common problem with b) is if you upgrade at the airport and only receive miles & TPs for your original booking class.