I'm just adding this thread to add to the google search helpfulness of the forum. I'm not sure if this is specific to X3 but this is the first time I've encountered it.
If you create multiple takes in a MIDI track using Sound On Sound mode (and perhaps others) and you open ONE of the lanes in the PRV all the notes of all the takes within that track will appear in the PRV window making it look like you have a pile of doubled notes.
This happens even if you mute the lanes no matter what your settings and will also happen if you mute the clips themselves by using Right Click > Clip Mute/Unmute unless you have set the following option in the PRV Views menu View (PRV Menu) > Hide Muted Clips.
I found this out after a bit of confusion. I had some live MIDI takes muted, clicked on the one I wanted to work on to open the PRV for that clip and saw a ton of doubled notes. I thought my controller had been sending doubled signals so I was going through deleting some of the doubles and went to audition the part yet some notes were sounding and others weren't I had no idea what was going on and thought the project was screwing up (what was actually happening was I was deleting the notes in the lane that was audible and leaving notes from ones that had the Mute button engaged). I decided eventually to create a new take that I play cleanly and left out certain sections but when I opened the PRV I saw notes in areas where I hadn't been playing at all. I went to through the various Views menu thinking that perhaps the other takes were being shown as well as the selected take and found the View (PRV Menu) > Hide Muted Clips option. I clicked that but the extra notes still remained. So I tried using selecting the muted clips > Right Click > Clip Mute/Unmute option and all of a sudden the extra notes disappeared.
So basically it was a lot of confusion and hopefully this will help others not get tripped up the same way.
To sum up:
If you open the PRV of a specific clip in a MIDI track by double clicking that clip all the notes of all the takes in that track will show up in the PRV creating a grand old mess.
Avoid this by:
1) Selecting all the clips you do NOT want to edit/view in the PRV
2) Hold Ctrl > Right Click > Clip(s) Mute/Unmute (this will mute the clips to make the next option work... you cannot just use the Take Lane Mute button)
3) From the PRV menus select... View (PRV Menu) > Hide Muted Clips
NOW you will only be looking at the clip/take lane you want to be working on. That last bit may already be set by default (I forget) but it's important.
One thing I'm noticing about X3 is some of the default settings are rather weird and I'm having to set things up that I personally feel should be set to more basic parameters. So just be wary of things like this I guess. Great version of the program but it's the little things that'll get you if you aren't paying attention to how the Bakers set things up by default.
Hope that helps someone. Cheers.