I am having this problem too, on multiple sites, with different themes. I have tested changing to twentyfourteen, disabling plugins, nothing is working.
The pages of Buddypress that are redirecting to 404 pages are Notifications, Messages, and Profile, maybe some others.
Groups, Members, and Activity work fine.
My htaccess has the same settings as a site that completely works.
I am also buddypress 1.9.1 and still having this problem on multiple sites.
On one site, Artisteer Themes don’t seem to support Notifications, Messages, Profile, although I may need to do some playing around to see if that is on all Artisteer themes.
Notifications are definitely displaying wrong on the Custom Community Theme.