Trust me when I say the combo updates are better. MacFixIt.com had a huge article about the combo updates. However, a subscription is needed to see the article. It short it talked about there are the full system programs updates instead of the small update only files found in the software update.
I use to have small problems all the time until I started using the combo updates and repair permissions after every software install. Since I started the combo updates I have had zero problems (crosses fingers and preys that this holds up) on my 2 1/2 year old hacked Tibook.