I have a three part answer here that, unfortunately, doesn't actually fully answer your question.
I've never heard those rumors specifically, but there is a long history of parents fearing the negative consequences of vaccines. A recent, and unfortunately ongoing, example is the completely baseless claim that vaccines are linked with autism. In fact, as I write this response, there is a google add that reads, "Test your child - Autism." I can only assume that google has placed that add there because there are enough pages on the web that talk about this so-called link.
Second part: Some of these rumors may stem from the fact that most vaccines (like the flu shot) are created using a modified version of the virus itself. Even though this may seem like a good reason to be suspicious of getting vaccinated, in truth, there is no chance of getting a disease from a vaccination (though, apparently, sometimes side-affects can occur)
The last part of my answer is totally 100% conjecture: there are some pretty powerful interests out there who would like to see the HPV vaccine go away. These "interests" do not like the idea that we can vaccinate against an STD and thereby remove some of the risk from non-marital sex. Are these "interests" above spreading rumors to undermine the vaccine? I don't know. I do know that, for example, right before the 2000 election, several hundred flyers were found underneath the windshield wipers of cars in a low-income neighborhood reminding people to vote on November 8. The problem? Election day was November 7.