seeing the different comments about the fender on/off got me to thinking about the rear shock possibly being the variable. Its a fairly tight fit getting the front wheel in/out with the fender still attached, you have to get the front as high as possible by making the rear wheel hit the ground in the back. If you're running an aftermarket shock with a slightly different overall length, that would affect your ability to raise the front wheel, and might be the difference between having just enough clearance, and not enough.
Years ago, after seeing how fast the ST fork oil turned to mud, I started changing my fork oil with every front tire change. So I usually take the fender off anyway in preparation for removing the forks.