Whirledtraveler - Congrats on post #10,000.
I too am curious as to which routes didn't clear and just how far in advance you booked them.
On March 6, I booked a netsaver for SFO-HNL (where i am now) March 8 - March 10, I put the reservation on hold, check the boxes for upgrades and both requests cleared immediately. I had never had this happen before.