A major reason for the current USPTO budget shortfall is the dropping rate of renewal. According to the USPTO annual reports, the "maintenance fees have traditionally been the largest category of patent fees." Renewal rates are charged in three-stages. The first-stage payment of $980 is due 3.5 years after issuance. The second-stage payment of $2,480 is due 7.5 years after issuance. And, the third-stage payment of $4,110 is due 11.5 years after issuance.
In FY2009 renewal rates dropped for each stage. Most troubling for future PTO revenue, the first-stage renewal rate for FY2009 was the lowest in a decade. The graph below is based on historic USPTO Annual Reports.