Main site rewrite not working

I’ve installed MU using sub domains… I have a couple custom post types along with single post pages. On a normal install the permalinks work as expected… http://brewsters.ca/Beers/farmers-tan-white-ale/ with a page called single-Beers.php. But with MU the main blog resolves to day/month/year/farmers-tan-whie-ale which throws an error. I’ve tried changing the permalink but no combination works.

Question I’ve had issues with uppercase naming with certain providers… could this be the issue?

Or

If this is normal is there a way to change the rewrite to make it consistent across all the networks?

All help is much appreciated.