Ahh yes, the classic admin vs developer debate. I love this kind of argument. Both insist they're right, when, in actuality, both are somewhat wrong.
Let's start with the obvious:
#1: Clear out your .htaccess in just your whmcs folder. Let's make sure you don't have anything silly or custom blocking access to it. Save the contents somewhere else.
#2: Repeat step 1 for your public_html folder (if your whmcs folder isn't directly in public_html itself)
#3: re-try. If this works, then yay, good to go. If not,
#3a: open up a file in your whmcs folder, call it test.php. In there, put the following code:
print("I am a test script");
#3b: Save the file, and try calling it from a browser (ie:http://www.yourdomain.com/test.php). Did that work? If not, then there IS a problem with your server/account configuration. If so, then you need further assistance from knowledgeable server administrators. Arguing that "there's nothing wrong with php.ini" is kind of lame for an admin.
I can say that I've had zero issues myself with php and WHMCS that Matt hasn't been able to fix immediately. You might consider talking to him, but try to see what's screwing up in php.ini first, make sure it's not a global thing.