The whole point of speaker simulators (well, not the WHOLE point, but a particular one) is so that you don't have to mic up an amp. If you're going from the amp straight to the computer you're missing part of what the amp expects you to have for it to sound good. Guitar amps aren't like hi-fi amps, they are designed to colour the original signal and work in tandem with speaker. The sound of a speaker is part of what makes the guitar amp sound right, so missing it is never going to sound as good, unless you simulate that speaker with a special effect box (like a POD). Of course, I still don't think it sounds as good, but they get you there. Now, about whether that addresses your original problem, the answer is "not really", but I wanted to clear that up.
"Dozens of people spontaneously combust each year, it's just not that widely reported".