dir rewrite confusion

I’ve got several layers of WP installs.

root (blog one) 1.5b1<br />
--sub 1 (blog 2) 1.5b1<br />
----(layer 1 [blog 3]) 1.5b1<br />
--sub 2 (blog 4) 1.2.2<br />
--sub 3 (blog 5) 1.2.2

so is the root install and the 1.2.2 installs are just fine.

but the sub, and sub/sub installs of 1.5b1 get their url rewrites confused.

most of the installs are written into sub domains
ex: blog,domain.com

What i’m having trouble with is the alternate main domain:
domain 1 is fine: maindomain.com
but domain 2 is messing up: otherdomain.com

somehow livesearch isn’t searching, and unless i carefully close up the address’ with a “/” then it actually rewrites otherdomain.maindomain.com

it’s messing with my brain (small as it is)

does anyone have any clue where to even begin looking into how to solve this?

F.