URL without index.php cause timeout but with index.php works fine

I have a php script that runs for long time continuosly.

It is installed on a domain for example: http://ift.tt/ME9KXX

My issue is that whenever I try to open script through this url:

http://ift.tt/ME9KXX then my page shows timeout error after few minutes.

But in other case if I run the same url with index.php at the end e.g. http://ift.tt/1Jxz3LX then that works like charm for hours without any interruption.

Why is it showing such strange behaviour. Both urls access the same index.php then why one url works perfect and why other causes timeout?