You need an attorney.
Normally, there should be a way to prove payments - cancelled checks, etc.
Collection of debts can take many forms. I've never heard of anyone shortstopping GI Bill benefits, but it may be possible.
Certain courts will order a Father to bear responsibility for part of the costs for pregnancy, it appears that this Father did so voluntarily, Additionally, he was voluntarily make support payments in 2007, he would receive credit for whatever payments made if the payments were made during the same time that the court order for child support was pending. However, in the event that he was voluntarily paying in 2007, and then stopped, and then in 2008, she requested child support, and that order was made effective prospectively, then he may not be able to receive credit for those payment voluntarily made prior to the 2008 child support order. Consult with an attorney when you figure out the time-line of those payments, and orders.
As to being stereotyped as a bad father, most likely this was not the case. Child support orders are very non-emotional, and judges do not have much flexibility with respect to their decisions as to child support. Start thinking logically and talk to an attorney about whether or not you were entitled to credit for the payments made prior to jumping to the conclusions that a judge is treating you unfairly.