The explanation you got from your boyfriend isn't possible to happened.
With HPV vaccination you are protected for the most common HPV strains that cause genital warts.
The same vaccine has effect in males, too (but, before being exposed to the virus).
It is good to know that the incubation period (period between being infected and initial symptoms) for genital wart is between 3 months and 2 years.
Proteins in urine can result from benign factors as fever, intense activity or exercise, dehydration, emotional stress or it can indicate more serious conditions like kidney problems.

Best wishes!