I looked throughout the forums for a solution to this and tried a number of things, but have given up and added my wail to the wall.
I added buddypress (1.2.3) as a fresh install (original buddypress theme) in a /community subdirectory of http://www.venture4change.com. (2.9.1 I think) Everything works just fine.
However, buddypress seems to take over the nav links of the root site. I tried changing the blog address, and also moving off the original bp theme. No luck.
In addition to suggesting a fix, could you explain to me why this is happening?