The front's the only 'effected' input from what I've read, but I could be totally wrong - such is the nature of proprietary matter.
Question for those in the know as well - is the front input's circuit physically different or is it just the special sauce algorithm that makes it different from the rear?
edit - found this clip
Cliff: "You have to set the input selection to match the input you're using. If you're using the front input then you must set the input selection to front and vice-versa. If you plug something into the front and set the input selection to rear it will get MUCH brighter. The front input is optimized for guitar-level inputs and has spectral shaping and more gain than the rear input. The front input is optimized for guitar pickups. This is a combination of hardware and software processing. If you set the input source to Analog Rear this turns off the software processing part. If you are plugged into the front it will change the tone since you're still going through the hardware processing. This is why I say you must match the input selection to the input you are using. The rear inputs are standard line-level inputs and can be used with any program material. The front input, as stated above, is optimized for guitar pickups. As such it has more gain and less headroom and may clip if used for non-guitar program material. If you plug a guitar directly into the rear you may find you don't have enough signal level."
from this thread:
http://forum.fractalaudio.com/axe-fx-ii-discussion/48798-inputs-question-soft-clip-normalize-3.html