Kohana is known to have issues with safe mode. Generally speaking, any decent host will have safe mode off, because it is simply an annoyance.
Source: http://forum.kohanaphp.com/comments.php?DiscussionID=5062&Focus=35961#Comment_35961
SafeMode will restrict a number of PHP functions, and as i understand it, is used on shared hosting environments where the hosting provider has to restrict the use of these functions to prevent people from messing up the other hosting
Source: http://forum.kohanaphp.com/comments.php?DiscussionID=5062&Focus=35954#Comment_35954
phpBB3 same, cache files are written to 99. But phpBB3 read/write/delete own cache, why KO3 is not?
Source: http://forum.kohanaphp.com/comments.php?DiscussionID=5062&Focus=35945#Comment_35945
Something has to be messed up with your apache. When it creates a folder it should have permissions to that folder, which sounds like it's not doing.
Source: http://forum.kohanaphp.com/comments.php?DiscussionID=5062&Focus=35941#Comment_35941
ErrorException [ Warning ]: file_put_contents() [function.file-put-contents]: SAFE MODE Restriction in effect. The script whose uid is 522 is not allowed to access /home/mysite/application/cache/7f owned by uid 99
Source: http://forum.kohanaframework.org/comments.php?DiscussionID=5062