Your RewriteBase is wrong. This is from the Knowledge Base:
Do you support search engine friendly URLs ?
Yes, search engine friendly URLS are supported, but there is one important thing you must know: We use virtual user directory paths, so you can get error when trying to setup search engine friendly URLs or trying to pass virtual directory names to PHP scripts. If can be fixed very easy. Edit your .htaccess file and add this line at the top of the file or before the first rewrite rule:
RewriteBase /
Note: if your script is installed on some directory, for example /forum, you have to place RewriteBase /forum/ line to the .htaccess file (.htaccess file must be also located in /forum directory)
Besides that Kohana 3.3 also introduced support for PSR-0. So go through all your files in APPPATH/classes/ and rename them if necessary. For example: APPATH/classes/Controller/admin.php
should be APPPATH/classes/Controller/Admin.php
.
That should be it. If your kohana folder is currently inside the /public_html
folder you might want to do something about that. It's a good idea to put as many files outside of the web root when possible.