I have 2 blogs on my MT install. I am using MT 2.64 on Apache 1.3.27/mod_perl 1.26. (Using the mod_perl config of MT.)
Recently we discovered that the calendar for one of the blogs was linking to articles in the other blog. I think this occured just after a post (meaning, the calendar was rebuilt.)
My theory is that this is a mod_perl global problem -- i.e., MT is relying upon globals (or file-scoped lexicals) to store state data, and so later clicks (landing in the same apache process) are inheriting values from earlier. I haven't looked at the code to verify this though.