I had some trouble creating folders or uploading content via the CMS, and thought I would post about it here - if this isn't the right place to post it, please let me know.
When I was creating folders, the CMS would register it fine, but the underlying filesystem wouldn't show the new folder - turns out it wasn't creating it in the first place. The CMS should have picked this up but didn't, so that's a bug, but I don't know how to register bugs, so I'll leave that for someone else if they are interested (or let me know how and I'll throw something in the bug register).
Basically my host (I have a Media Temple (dv) account) uses a different username for the apache (httpd) process to the PHP process. Thus, when uploading, apache was doing the work and would create the temporary file in the silverstripe-cache folder, then PHP would come along to copy it to the right folder but wouldn't have permissions to.
For the folder creation issue, again because of the different usernames of the processes, safe_mode was stopping PHP from doing its thing.
Anyway, sorry for the short and not very detailed message, but something to watch out for there.