Oftentimes frame flex or even a little tug at the shifter cable can cause the gearing calibration to get off. Then, you'll hear grinding in some gears. So, whenever the Shimano IGH gears get a little crunchy, always check that your gearing calibration is okay. If you don't know what this means, then check out: http://www.sheldonbrown.com/nexus-mech.html

Hopefully, this is the problem and not something major. Good luck!