thorneven

I downloaded that and installed it and I cannot find it anywhere. I went to the folder where it's installed and all there is is an uninstall executable.  I'll try a reinstall.
 
For one thing the install dialog says it gets installed in C:\Program Files\Line6\Line 6 Updater which is totally wrong.  There is no Line6 folder in /Program Files, and there is no Line 6 Updater folder in /Program Files (x86)/Line6 folder.  I also told the installer to create a desktop icon and it doesn't do that either.
 
UPDATE... OK, it all worked when I did the reinstall.  Yay.

Be careful with 009's.  I used to use them on my Fender FMT Tele and found that because of the medium-sized frets, I would cause my guitar to go out of tune when I pressed down too hard on the fretboard (you know, in the heat of the moment).  Since the frets on the JTV59 are similar, I go with 010's.

It is normal. On any "standard-tuned" 12-string you play in a retail store, you'll hear that the two B strings play the same pitch and the two high E strings play the same pitch.