404 IE and No Input FIle Specified – Mozilla Chrome

Here’s the problem I have been struggling with for more than a week now. It is an intermittent problem therefore very hard to nail down.
Sometimes when I go to view any page including back-end ( admin area ) pages I will get a 404 not found error on IE or input file not specified on Firefox and Chrome. I haven’t bothered trying it on opera 3 out of 4 is enough.
I have searched forums here, google searched it and this is a last ditch effort.
Things I’ve tried:

• Changed permalinks from /%category%/%postname%/ to just postname
• Checked and double checked .htaccess then checked it again
• Double checked my coding a few times

I have several sites that I manage and maintain all with basically the same configuration and plugins hosted with the same company. This is the only site that is doing this.
If anyone has experience with this problem and can offer any help or a solution or links that might point me in the right direction I will forever be in your debt.

Thanks,
CT