The 12 minute tune gives your bike's computer a chance to "learn" the air/fuel ratios and ignition timing required for optimum running at the altitude you are at.
It's typically not supposed to be needed unless you do a slight mod, such as slip in a replacment K&N air filter, or something that slightly alters the air/fuel ratio. Typically, your bike should make these adjustments on the fly, so you should rarely have to do a 12 minute tune.

However, as Britman also stated, I have found that if I do the 12 minute tune every 6 months or so, it tends to correct any idle surging problems that may develop. Now, Britman and I are both running PC-IIIs with the O2 sensor by-pass, so this nay be part of what we are experiencing.
 
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