Problem linking from form back to site

Ok, so heres the problem I'm having... i can access the chronoform i created on my website no problem, but the issue I'm running into is that when I attempt to navigate the rest of the website from the chronoform page It gives me a 404. For some reason when I'm moving back into the rest of the site an index.php is placed between the domain.com and the category. So it looks kinda like this:
http://website.com/index.php/category
This isn't a problem with the "home" menu item since website.com/index.php does exist there, but yeah... Thank you very much and any help would be appreciated.

Oh and I'm not sure if this matters but I'm using chronoforms v3.0 beta 2

Hi jbush,

let me ask you a question, do you have SEF ON ? if yes then turn it OFF and retest ?

lets make another experiment too, backup any forms you have created and uninstall V3 and get V2.5, does the problem still happen ?

Thanks!

Max