installing 3.0 beta2 causes issues with permalinks and mod_rewrite error

[anointed]

For some reason when I install 3.0beta2 I end up with an 'index.php' in the middle of all the permalink choices given to me.

My best guess is this has to do with apache mod_rewrite saying it's not activated ​http://core.trac.wordpress.org/ticket/12255

I am absolutely positive that mod_rewrite is indeed active. I am running numerous 2.9.2 websites on this server and do not have this issue with any of them.

Just to test it further, I erased an install of 2.9.2 from a current site, and replaced it with 3.0beta2, and it also gave the same mod_rewrite error when trying to activate multisites. Also had same problem with permalinks, which was not there with 2.9.2

Is this a bug, or just a stupid error on my part?

[johnbillion]

Possibly related: #13106

[wpmuguru]

This is a result of r14051. Prior to the change the index.php prefix was set after processing the post rather than before.

[dz0ny]

Seen before as (​http://core.trac.wordpress.org/ticket/13021)

[nacin]

[14732]

[wpmuguru]

Can we get some testing feedback on this one?

[dd32]

See #13106