Bumping this old thread because I have the same problem. And I'm not running XFire or any other software that should be messing with the mousewheel.

Mousewheel doesn't work with three different mice (Logitech B58, Microsoft Standard Wheel Mouse, Logitech MX Revolution). Mousewheel in JA2 doesn't work with either standard Microsoft drivers nor with the Logitech drivers. This is on Windows 7 64bit.

I'm fairly certain it's not the mouse. The only thing I can think of is that possibly the Lenovo software which is embedded in the Windows Setup on my Thinkpad may be causing it. However, the mousewheel works fine in every other application or game.

It would be awesome if some alternative keybindings for aiming auto/burst would be added. I recently talked to someone in the IRC chat who has the same problem, so this apparently affects a few users.

Take a look at this thread. Similar mouse problem with a fix:
http://www.ja-galaxy-forum.com/board/ubbthreads.php/ubb/showflat/Number/321048/Searchpage/1/Main/21076/Words/glitch+windows+7/Search/true/Re_1_13_Mouse_wheel_issues.html#Post321048

As this issue seems common, I added an alternate keybind: As of r6555 and GameDir r1855, if USE_AIMED_BURST and AIMED_BURST_ALTERNATE_KEY are TRUE, then [Alt] + [t] over a target will toggle aiming.

Yes. But I needed a single-key keybind, as we cannot use any combination using [CTRL], [ALT] or [SHIFT], as these interfere with what the mousewheel does. The option menu shortcut isn't tha important. Furthermore, only those without a working mousewheel have any need of this, this is off by default, in which case the button works normally.