Can the IRS charge a penalty for filing late 2 weeks on a s corp. They charged me 975.00 for the 2011 but 89.00 in 2009?

Can the IRS charge a penalty for filing late 2 weeks on a s corp. They charged me 975.00 for the 2011 but 89.00 in 2009?
Absolutely... request a copy of their calculations to determine the difference. It more likely than not has to do with the lateness of the returns - 2011 was probably filed much later than 2009.

A decent CPA should be able to get some of the penalties knocked down, if not abated, for you.