Did you swtich from CBSE to State for 11 and 12th? Have you completed your graduation or have to stopped at 12th passing.
You have done what many student do called as Improvement examination. For CBSE students, improvement exam is allowed only once in the following year. In your case CBSE 10th in 2010, should be followed by CBSE 10th improvement exam in 2011. So, giving two exams is not illegal, only you have lost one year.
I'm presume you chose state board with an idea or scoring more marks. There are no stringent guidelines for state board that I know of. In CBSE, you have to have keep both marks card.
As long as you statisfy the legal age criteria for taking 10th and 12th it should be fine.
Please approach the 12 college office and clarify once. But you need to have both certificates in hand and produce whenever anyone asks for it.