this is a problem I encounter a lot recently. I know, when updating themes etc. I have to add (in SS 3.0) ?flush=all or ?flush=1 to the URL. Now, when updating the live version online, this simply does not do the job. I do see my /tmp folder getting new sess_* files but user on other PC's don't see the result, only 500 internal server error pages, while, if they ALSO add ?flush=1 or ?flush=all the problem vanishes for them. But offcourse, I don't expect my random visitors to 'try' this. Is this a known issue?
Ah, well maybe I called to soon. It seemed that my cache directory was way out of my legal position on the vhost of my provider. Adding the folder silverstripe-cache to my home directory of silverstripe installation fixed this. Hope this is useful for future reference.