I would say there are several things I would try right off and a few things to note.  The software in most to all cases is fine.  The sound you are hearing is because of the "Tone" and Level of that setting.   This will involve a few things to fix and would change your over all sound but probably for the better.  This has happened to me.  It involved "Hot lines" and Hot Pickups.

First if your line is running "HOT" you need to turn down that line noise.  Hot lines make strange sounds in the digital world that you can only hear often with a good pedal or amp.  You need to "Pad" the line.  Or reduce the voltage.  With many types of pickups this can happen to your tone.  You may hear fuz when it pugged in.  Its also improtant to use the correct cables.  A guitar cable is not a cab cable!  get a 12, or 14 g cable to that cab from the amp.  Dont think it matters.  "Wrong" when you turn it up, or add comp to that setup for the first time you will start to notice things.     If both of your guitars are powered pickups you will want to start with this "PAd" idea and then move on to other checks. 

Can you... "PAD" the Amp.  On my Swr working pro 700 there is a "Pad" button.  I hit the Db reducer next to the input.  Dont have that?  well, some have that on the out put for line noise, not that that whould help here.

Next Dont crank your vol level on your guitar.  Turn it back a bit.

Look to make sure if its Live that Verb did not get bummped.

Hope that helps or gives you ideas!

happy jamming

John- Band:  Kill the Sky