PHP stops after exactly 46 seconds - php

Question

I have seen many topics with a similar question, but not a similar situation, because the php settings do not seem to be the problem.
The current php.ini settings are:
max_execution_time = 600
max_input_time = 600
memory_limit = 512M
post_max_size = 192M
upload_max_filesize = 192M
These settings cannot be overwritten by the local .htaccess
The script
The script is PHP and does the following:
User uploads a movie file (using uploadify).
Once the upload is finished a script uses ffmpeg to convert it in to a lower quality 480p flv file.
The problem
This script has always worked and since the upgrade from php 5.3.9 to 5.3.17 it has stopped working.
The upload part works fine. I have tried it with 1Mb to 190mb files.
Once uploaded the conversion starts and the script always stops at exactly 46 seconds. I have no clue why, but it is always 46 seconds.
The server
The server is a xeon quad-core 16Gb ram and a load average of 0.62 (8 = 100% cpu usage)
I truly have no idea what the problem seems to be. The script worked fine and has not changed. So it must be something to do with the new PHP or perhaps Apache, but I have no clue.
Does anyone have a suggestion regarding what the problem could be?

Answer 1

Check the TimeOut settings for Apache, or add this in the VirtualHost section:
TimeOut 2400
You can also check if it really is a timeout or maybe an other problem (like memory) by making a script that sleeps for 47s:
<?php
sleep(47);
echo "Hi I'm still alive!";

Answer 2

Solution
Thanks to Nin, I found something in my apache error_log and was able to fix it:
Login to WHM > Apache Configuration > Include Editor > Post VirtualHost Include > All
and add
<IfModule mod_fcgid.c>
FcgidProcessLifeTime 8200
FcgidIOTimeout 8200
FcgidConnectTimeout 400
FcgidMaxRequestLen 1000000000
</IfModule>
It seems to be a fcgi problem.