I have been playing Rocksmith for a while now, but generally use just one guitar.  I noticed that I do not miss as many notes/chords using my Stratocaster as I do my Dean Vendetta (Locking nut floyd rose) or my Les Paul electric/Acoustic guitar.  There are times when I see a miss show up on the screen and I know without a doubt that I did not miss that note/chord.  So I am wondering, did I calibrate the game with the Stratocaster and the other two are significantly different that the program does not recognize the note/chord because of the calibration?  All three guitars are tuned the same, but their action is similar, but not exactly the same.  They are all intonated the same and have about the same relief.  They all have different coils though.  Obviously, the Stratocaster has single coils, and the other two are humbuckers, but I can split the coils on the Dean and it did not help.

 

Any others have this issue or have a few ideas?

Always recalibrate if you change guitars. Output volume of guitar can be significantly different from one to another and the game can't know which guitar you are using which might induce some problem in recognition when switching guitar.