Well this is very strange. If the path and file is correct it should be loaded and reported in phpinfo() as:
Additional .ini files parsed /home/snoturtle/.php/5.3/phprc
But it isn’t. Crazy stuff.
You’re not putting the .php directory inside the domain directory are you? (I doubt it).
Check the contents of phprc and make sure there are no errors inside it. Remove everything except the following:
upload_max_filesize = 50M
post_max_size = 50M
PHP running as php5.cgi is also puzzling. If it’s loading 5.3 or 5.4 then the version should be reflected in the running cgi.