A reinstall is unlikely to fix it, it's a dastardly bug. You may also have lost Sun Glare at the same time. (Sun will just be a pinkish yellow disk with no glare).
There's a fix that allows you to run the game in higher resolutions under WinXP and another for WinXP with Service Pack 2. If you do this fix and run at higher res, you can get sun glare back, (I have sun glare again, finally, running the game in 1280x1024). Here's a link to the Resolution fix in the SH3 Community Manual in case you're interested:
http://www.communitymanuals.com/shii...lay_Resolution
For smoke, I've had good luck alt-tabbing out of the game, and right back into the game to restore normal smoke. Problem is, sun/moon glare (and some other things) will then just kill the smoke, but I've found if I alt-tab in and out of the game quickly while looking at the moon or sun, then smoke will stay. Strange, but it works for me every time.
May seem like voodoo, but there ya go.