In my case I had duplicate GPUs pulled for an October / November round trip to Sydney. The trip was upgraded from W to business.

Online my "Account Details" page under "Most Recent Account Activity" shows two identical entries reading as follows.
"03/03/2012 12:01 a.m. System-wide Upgrade Redemption (1)"

Note also that the term "System-wide Upgrade" was used instead of GPU terminology.

Seat assignments remained correct on all six segments of this itinerary.

CB