I had this problem too. The issue for me had more to do with the quality of the sound card I was using. I recently upgraded to a RME FireFace 800 (
http://www.rme-audio.com/english/firewire/ff800.htm) and now, my direct signal is clearer and punchier
A few things are at play here that you may want to look into. First, the analog to digital conversion taking place in your sound card. It colors the tone quite a bit more than people may realize! Second, the way the direct signal from the guitar is brought up to line level. Because the signal from the guitar is VERY weak it has to be amplified to reach an appropriate level for recording. This amplification takes place either in a D.I. box or within the audio interface itself. The quality of amplification and process it uses changes the tone considerably.
Turn off all of the amp modeling at your input and record your direct signal only to RiffWorks. You should hear an acceptable sound with clarity and good attack. If it sounds muffled, less defined or unclear to you then it may be time to upgrade. It really depends on what you can live with but if the signal going IN to the amp modeling is not clear and defined then the amp models will only accentuate the problem and make it worse. It's not really something you will be able to EQ away.
I think what may be happening (cuz it happened to me!) is that you are getting pickier about the quality of your tone so you are trying to capture a better signal. The TonePort has decent converters and inputs but nothing spectacular. I certainly wasn't satisfied. What ruined me was actually hearing what a clean guitar signal COULD sound like with higher quality components.
Another solution you can try is to buy an active D.I. box that is higher quality like the Radial J48 (
http://www.radialeng.com/di-j48-features.htm). This will give your guitar signal a clean boost and bring it up to line level before you send it to TonePort. It can have a HUGE effect on tone. IF you go this route just make SURE you output from the D.I. box into the "Line Input" on your TonePort. It would defeat the purpose if you go out from something like the J48 and then right back into the high impedance guitar input where the sound is re-colored! At this point, I might be confusing you?
It all comes down to money and how much you want to spend to get closer to that "perfect" tone. But the differences are insubstantial to many who would never know or care. You are entering some dangerous territory on this one :O
Rich