When you submit a FAFSA, it goes through a number of data matches with other government agencies, such as social security and the department of homeland security. It's not saying that you aren't a citizen--it's just saying that for one reason or another, the data didn't match up so they can't determine what your citizenship status is, so you need to provide a document to the school to clarify the issue. Often it's because there's a difference in the spelling of a name, or because the change occured recently and the database hasn't been updated yet. The school can't disburse your aid until you submit the documentation, but in addition to that, most schools will also look at the rest of the information on your FAFSA to make sure it's correct. So, it isn't just a matter of dealing with just that one document that you turned in.
As for why it's taking so long.....at this time of year, schools are swamped with applications so if there were 1,000 other FAFSA's ahead of yours that they have to look at, it's entirely possible that they just haven't gotten to it yet. There were also significant differences in how verifications must be conducted this year, so many schools are running behind because they had to revamp their computer systems to accomodate the changes. Also, parents could not file their tax returns electronically until a couple of weeks ago (due to changes in the tax code that Congress didn't vote on until the end of the year). All that adds up to a big logjam that means schools have heavier than normal loads of verification work to do right about now.
You can explain your situation to them, and maybe they'll be able to get to yours sooner, but most likely you'll just have to be patient.
Lawyers are like stop signs. On every corner, just look