Hey there this is a problem I had as well and was able to fix it easily. If you copied and paste the code for your comments.php page from the custom_smilies istallation page the code:
<?phpif ( function_exists(cs_print_smilies) ) {cs_print_smilies();}?>
is wrong there should be a space between php and if like this:
<?php if ( function_exists(cs_print_smilies) ) {cs_print_smilies();}?>
That seemed to clear up this issue for me! Hope it helps!