In some tones more than others (when gain is higher), I hear a noise even when I am not playing, like I'm touching my jack when not plugged in. RS detects something even if I mute my strings the best I can (I just mute them all, I am not trying to play clean). I have a decent guitar recently bought so I don't think that is the problem; the guy that sold me the guitar is absolutely trustworthy and good at fixing any issue a guitar can encounter. Is it some option (in the .ini file also) that could help me getting rid of this noise?

I have it too on some songs. I usually just use another tone with less gain.

I had the same issue (beginner player here), how do you change the tone on a CDLC?

 

I was able to fix this by turning the tone knob down all the way on my bass.  Just have to remember to turn it back up when I play a song with a better tone :)

 

There were several CDLC that I deleted because of this.  I went back and re-installed them after I figured out the tone knob trick.  But if there's a way to change the tone in-game I'm all for that.

Try the sound designer for that. You are able to choose some of the tones from any song you have (or your own crafted tones) and set them in buttons 2, 3, 4. In game you just click the button and tone will change for the entire song. If you click 1 (default tone) the tone will return to normal. Note that not using the default tone the song won't be able to do the "auto-tone changes" predefined for that chart. You can also use this in menu or session. 

Recalibrate your guitar!  Turn the volume knob down just a hair when you calibrate, and if you have dual humbuckers, move your pick up selector to both.  When you mute your strings don't hold them, just tap to mute, and let it play out if there's anything still ringing, after that go through the motions tuning up, and then after all is completed, switch back to your bridge pick up, and turn the volume up.  I promise that will help.  Another thing no one has bothered to mention is the RS realtone cables suck my ass!  Personally if you have a soldering iron, or if you're patient enough with electric tape.  Chop the head off the RS cable (jack end)  Go buy you a 90 and solder, or tape it to the new head!  That helps a ton.  Aside from that man RS isnt 100% perfect.  But try downloading, or creating, and saving some new, or your own tones.  It helps when there's shitty CDLC tones on a particular song you might like.  That way you don't have to endure the overly sensitive piece of shit sound the cable causes the game to make!  Cheers!  Oh, and fyi!  If you move your pick up selector to the neck pickup, and tune it that way before switching back to your bridge per say.  it helps alot with the accuracy of tuning.  SO I'VE HEARD ANYWAY.  I do it all the time, but I dunno if it makes a shit or not.  lastly if you haven't or aren't sure.  INTONATE your bridge!  Cheers bubba!  Let us know what you find out.