I've found the following things are critical.
1) You want the input gain/return volume to be at 0.0 on the Kemper, futzing with this or other settings to anythign other than noon seems to result in poorer profiles. SO just adjust gain outside of the unit.
2) How are you playing this back? If it's through a mesa amp FX loop you may have issues as they run in parallel with a blend unlike most other FX send/returns on amps, which means you always have the original sound coming through too to a certian extent (minimum 10% of the signal I believe). Also how are you recording to compare the signals?
3) Two short sessions followed by a long, as in at least 10 minutes refining session seems to do it for me.
4) Remember that more volume at the amp end is always better when it comes to noise floor, but compromises dynamics as it begins to add compression, balancing this is a must.
5) Sometimes you have to give up on the first profile you do and just move on and start profiling all over again, I'm not sure why this is (maybe a bug in the KPA), but the first time can sometimes just muck up, the subsequent profile you make by simply pressing the new profile button rather than switching the chickenhead switch back and forth from profiling mode (important that you don't do this) will be much closer. However I only do that the once, if the second profile fails then I just continue refining.
6) What you play during refining matters. If you have large gaps of silence then it will adversely affect the profile, so play solidly. Play a range of things, chug chords, palm mutes, open chords all over the neck, lead lines etc. Just playing one thing has never worked for me, play both light and heavy rather than all just hammering the guitar in a frenzied attempt to break the strings, unless your aim is purely to record a cover of helter skelter of course.
7) Even though this is DI, it's still worth making sure to record the signals direct into a DAW and ideally do a reamp of a dry guitar signal that you record to compare both the KPA and the original amp using the switch on the KPA as otherwise listening through speakers with both going and while you can hear your guitar strumming too will never give you a clear picture.
8 ) The result from a DI will have it's own cabinet which is a part of that sound. Disabling it will give you what the KPA thinks the preamp on it's own sounds like (the cab seems to represent power amp and cab), but often that's not necesary. Don't disable or replace if your'e going through the same setup as the pre-amp was originally.
Anyhow, I hope some of that helps.