This is still a problem for me, and I am running latest Evernote client on Windows XP SP3. Not just Win7! Very jarring, because I am accustomed to using mouse wheel scrolling for everything, and it works fine everythwhere else. I am using no custom mouse software or drivers or settings--simply built-in Windows driver for PS2 mouse.
This would be the single most useful addition to the clipper I can think of. Combine with a "Open all links" command within Evernote to get the list of clipped URLs back into the browser, and we have a WINNING way to manage web research projects. It's so close I can taste it! :-)