I believe you are the 4th person to confirm that, and yes it defies all logic.There might be something to that... I've ridden it the last couple of days and it seems to be back to normal - which defies all logic to me.
It did go the better part of a month without being ridden, but I'd expect it to run the same regardless of how long it sat...
That information also blends well into the fact someone else said there was a intermittent (on/off) 60mA drain on the battery i.e. it could be that for a week the systems are powering up occasionally and keeping whatever settings the bike has learned up to date, but after a period of time (3 weeks?), or certain voltage/watt.hour has been reached that it goes back to default. At some point someone could experiment by leaving a battery tender on it perhaps, or perhaps let a 650 sit for a month but let it re-learn things by letting it sit idling for 5 full minutes so it can re-learn things a bit.
I had a Toyota Tacoma that would change the shift points based on how it was driven, and it used to drive me nuts that it kept shifting between 2 gears about 29mph. 28mph and any press of the accelerator at all and it would downshift, 29mph and backing off on the accelerator would upshift. Drove me nuts because at the time a large % of the time that was the speed I wanted to go. Disconnect the battery and it went back to factory defaults and it stopped doing that for a week - but the radio presets were lost.
I sold the Tacoma because of that and other nuances, however my TR650 has a *lot* more soul (and at the moment is more practical) than the Tacoma was.