I would canonicalise the index.php and non index.php versions to avoid duplicate content here and ensure that the weight is combined into one version.
You may find that your rankings have changes as a result of this redirect process based on IP.
As far as I can see, any links that point to your homepage go through this process:
link -> www.mysite.com
--301--> www.mysite.net/index.php?country=usa/uk
--301--> www.mysite.net/index.php
This is going to send the links on a chain of 301's eventually ending up with duplicate content, which isn't best practise. Hopefully someone else can chip in on this one and advise if this is the case and potential solutions.