Last night I petitioned the "bugged" raid we had, and asked the GM specifically to check the server logs and verify weather we won or not, and to report the issue with the raid resetting after we finished.
The bottom line is, the GM said we defeated the raid, and he had no problem granting the loot we received. All we need to do is have the raid leader submit a petition, and identify who the loot goes to.
Attached is a PDF of the email string from the petition if anyone would like to read it.
We won according to the server, and if a GM says we won and is willing to grant the loot, the right thing to do is bid the items and award accordingly.
-Harden