I assume you're using an FHA loan..There was a regulation that limited the guaranty on these loans to buyers if the seller owned the home less than 90 days. It was generically called the "FHA anti-flipping rule." Since FHA backs these loans, the lenders have to follow their rules.
That being said, if this is the case, then your lender has not kept up with the guidelines. They may have other reasons for the denial, but if it's merely to comply with the 90 day possession guideline of the FHA, then you need to question further. In order to stabilize the housing market, the FHA temporarily waived this requirement back in 2010. The exemption from following the guidelines was set to expire in December 2011 which would have meant that the 90 day rule was re-instated.
But, the government extended the exemption again until December 2012 which means that the 90 day rule does not have to be followed. I would question your Lender or ask another Lender. Here is the link for the government extension of the exemption...