Thanks! Very helpful. It makes sense because it would seem that selecting Studio/direct takes it out of the filter. I had not noticed this, and the result is appreciably clearer.

I use studio direct mode into a Rocktron velocity 100 that feeds my guitar cab. This so far has been the best set up I have found. I run preamp models only with no speaker sim at all. I found that when you run out the pod via 1/4" with output mode set to stack/combo amp, the speaker emulation is still on ( when you use the cab emulation in the pod ), but with a slightly different filter. In studio direct mode no speaker cab emulation is realized even if your using it in your patch. However if you turn off the speaker cab emulation altogether and run out via SD ( studio direct ) or stack/combo they still sound different. The SD sounds to me more clear and focused, while the stack/combo setting still has some sort of filter. The two stack and combo modes have  two different settings. One for front and one for fx entry. The front has hi/low and focus parameters. I found them to be useless since I would not ever run this unit into the normal input of an amp. I almost exclusively used the stack fx loop mode during initial testing. Then I accidentally set the SD mode one day and noticed a nicer cleaner sound.

Here is my thought on why. When in SD mode the pod is supposed to emulate the patches as if they were exactly what they say they are. I.E. a Fireball pre should be the preamp of a Fireball..... So if I run the preamp of that amp into my real amp, I should realize as close to the real deal as I could get. No filters, no speaker emulation and nothing in the way to alter the sound. It should be at that point be preamp emulation, power amp and speaker cab. When in any other output mode the pod is trying to emulate and or compensate in some way for what they feel is needed.

I have tried running full amp patches ( minus speaker cab ) into my current set up and found it to not be as good as when using just the preamp. Although the sound is different and not exactly worse, I have found it to be too colored, bright and not as pleasing. I still have some experimenting to do running full amp and speaker cab emulations into an FRFR system, but at the moment for me it's still not quite there. I can get a sound I'm happy with, but I find it harder to build something that blends well in a full band setting for a live situation. close but not 100% yet.