Who replaced the VSM, the same dealer that scanned the system and found the polarity is reversed? Did he program the new module once installed? Assuming by "ford guy" you mean dealer, he should have the Ford tool that would allow him to get in to the programming mode, although I'm not sure if the polarity is a parameter that can be changed.

Assuming the "ford guy" is the one that installed the VSM, I'd ask them to go back through the reprogramming (as part of the labor you've already paid for) and doublecheck everything. Unless someone's mucked with the wiring, there's really no way for the polarity to be incorrect, it almost has to be a programming issue if the signal logic is reversed. Now if the issue is actually one of the doors is not changing states (and always reading ajar), that would be a different story. Their professional scan tool should be able to monitor each of the entry points independently.

-Rod