I'm struggling a bit to get a great reamped tone... It's pretty good but it lacks the last bit or so to sound great. I record a bit in E and Drop D with my standard axe equiped with a Duncan Custom. To my surprise though, when I noodled around a bit with my seven string with a Dimarzio Blaze it sounded clearer and with more definition (and more of the elusive "punch" :-) ) even though it's tuned to Bb.
It could be a lot of things... One is technique, I'm not an excellent player (only played electric for 4,5 years) - yet . But another thing is that I think the Duncan Custom might be too close to the strings and generates some subtle unwanted harmonics... I'm going to try lowering it and record again.
My main question though is how to tell if a DI recording is bad. If the problem is in my VST tweaking it's pointless troubleshooting gear problems (and the other way around).
Are you reamping, or putting an amp sim on the DI track?
Also - as long as you don't clip the DI track, and have decent level, it should be fine.