Hey,
I ran into the same problem with the release of vBulletin 4 and after seeing this post I decided to figure out how to get this to work as I used it quite heavily in developing skins for vBulletin 3.x.
I have tested the code I came up with and works perfect in vBulletin 4. I have now posted a new helpful tip and trick document on my support forums for all of you to be able to use.
Alternating Row Color for vBulletin 4 Skins [NON-Plugin Method]