Some configuration lines won't work with suPHP - at least, not within the .htaccess file. In particular, "php_value" and "php_flag" values are the two that are problematic.
So, in order to resolve this follow the steps given below:
First, you must move all lines beginning with "php_value" and "php_flag" from your .htaccess file into a file called php.ini (in your public_html directory). Then, you must add a line to your .htaccess file like the one below (of course "username" being your actual username).
You will need to remove php_value and php_flag from ALL .htaccess files you may have. However, you only need to add the suPHP_ConfigPath line in the .htaccess file in your public_html directory only.
Secondly, you must make sure that the lines you put in php.ini are in the correct format:
setting_name = setting_value
Let's say you have the following line in your .htaccess file:
php_value register_globals 0
the corresponding php.ini format is as follows:
register_globals = Off
Notice how the value 0 becomes Off (without quotes) and 1 becomes On. If your php_value has quotes like the following, for example:
php_value include_path "/home/username/cgi-bin"
The corresponding php.ini format is:
include_path = "/home/username/cgi-bin"