Well, this is interesting. All this time I've been researching work visas, when it turns out the main problem is the work permits themselves.
Back in the summer, the quota was reached. I'm not sure if my application got in before that or not.
"Effective immediately, the Federal Migration Service (FMS) of Russia will no longer accept Work or Employment Permit applications for foreign nationals seeking employment in St. Petersburg and the surrounding Leningrad region in 2008. The 2008 quota established by the government for St. Petersburg and the Leningrad region has been reached." -From "2008 Work Permit Quota Reached for St. Petersburg." Fragomen Global Immigration Services. Published online 8/13/08.
A St. Petersburg Times article about illegal immigrants observes how the new visa laws of 2007 have changed things. "In 2007, due to a tightening up of the rules regarding migrant workers, a number of companies decided to legalize their foreign personnel, leading to a 700-percent rise in the number of work permits issued to foreigners in comparison with the same figure for 2006, according to Daria Novikova, spokesperson for the St. Petersburg and Lenoblast Federal Migration Service Agency." -from "Firms Cut Costs Using Migrant Labor." March 25, 2008
Apparently, more work permits were needed in 2008 than companies had predicted. I fall into the same category as migrant workers, being a foreign national without resident status. I'm not sure if the quota was increased or not. It's one of the questions I will ask my boss. We are planning to speak by phone next week.