Is it to late to file for 2006?

In 2007 I used Tax Act thought the IRS, I followed all the instructions and submitted my efile. I waited for three months and I didn't get any response. When I called the IRS the agent said we have no records of you filing. So I have been spend all this time to make attempts to file it with a free tax preparation website and no luck yet. I am afraid that I will get in alot of trouble and I ave no extra cash to file at H&R. What can I do? I don't really care if I do or don't get a refund just as long as I do not get penalized.