I'm running many sites with custom php on ata3.6.4 and plan on keeping them there till i figure out the best way to update them all. in the mean time, Wordpress is will be rolling out version 3.2 sooo... my question is will there be conflicts that are know with ata3.6.4 and wp3.2? thanks.

I would assume (dangerous I know) that WP 3.2 will be backwards compatible with all themes, you just might not be able to take advantage of new features in WP 3.2 if the theme has to be aware of them.