If you're using php for your website, and you upload a customized php.ini file, BE SURE to set the file transfer mode in your FTP client to ASCII when you upload your php.ini file.  If you upload the file as binary (instead of ASCII), this can lead to odd problems with php execution, primarily the result of directives in your php.ini being ignored in lieu of directives in the server-wide php.ini. 

Consult your FTP client documentation on how to change the file transfer mode between ASCII and binary.  If you're using Windows command line FTP client, simply type ASCII or binary to change back and forth between modes.