I'm thinking that this might be a bug, but I'm so new to b2evo that it may, in fact, be pilot error.
I'm using a stub file to call b2evo & it appears to be working fine.
However, when I'm logged into the back-office, there's a an 'exit to blogs' link in the upper right, which (i think) should take me back to my blogs page ... instead, it dumps me off in the blogs FOLDER. (I'm thinking that if I was using an index.php file, this would be fine ... but because there is only a stub.php file ... I'm presented with a folder view, rather than being taken back to my blogs page).
This is not hugely critical, but I thought I'd mention it. If anyone has a work-a-round or if I'm off base, please let me know.
In your back office on your settings tab what do you have selected for "Default blog to display"? AFAIK the exit link will take you out of the back office to the blog specified in that field. My guess is that if you have 'none' selected it will go to your $baseurl setting in your conf/_config.php file, but that is only a guess.
I use a hack that 'exits to active blog' so I can't really say for sure.