Having looked through your information about the problem, Microsoft informs everything from a virus to various system file issues. Correction may be difficult, even impossible.
I would suggest zero formatting your hard disk(s), at least the main C, and re-installing Windows. Since your security didn't recognize the out-coming Trojan, you do actually form a hazard for others. We do have a responsibility for each others, thus we are obliged to make sure our own computers are safe, not only for us ourselves, but for others too.
Sorry to say this, but I think your computer is a risk. Clean it, please.