Virus? Software issue? Hardware issue? HELP!

My issues started over the weekend, I booted up, signed in then came the catch. I clicked on programs (chrome, explorer, Security Essentials) and it would seem to load for a moment, but nothing happened. Chrome opened, but would not search anything, no loading. I hit control alt delete and I got a black screen with an error message some like it couldn't load security. I loaded from safe mode and everything seemed to function fine. I thought it was a virus so I shutdown, and booted from a flash drive with antivirus on it (bit defender, and AVG) I updated them and ran each (separately) they found some Trojans and I removed them. Then booted from the hard drive again thinking the problem was solved, but nothing changed. I honestly have no idea what to do. If you need any more details, please just specify. Any help would be much appreciated.

Thank you,
Obese Armadillo