My employer did not pay my social security taxes in 2006 and for 2011 withheld too much and is not refunding my money.

How did they withhold too much?

You can file Form 843 if they are refusing to refund.

Withheld 6.2% instead of 4.2%

It doesn't matter after the fact if they over withheld. As long as what the report to the IRS matches what was deducted, you get it back when you file your return, not from you employer.