It might be a problem because they might have issues with ability to pay or the company to pay the prevailing wage. My advice is to find another company. On the other hand, you can still file with them and another company simultaneously. Note that H1B is closed right now, you need to file next year April 2010
Note: The above is provided for informational purpose only, one should not act or refrain to act just on the information provided. No attorney-client relationship is created unless a retainer is signed.