DaihatsuUhost

Regards people.
I have one very big problem and I need help.

I think I have a problem with name servers but I’m not sure
I have one Linux like hosting server where I keep all my websites. However, I have one problem.
Sometimes when I try to access some websites that are hosted on my server I just CAN’T get website to load. There is no ERROR page just like there is no page at all that address and like there is no that address registered.
Server is up and running and I now that because when I go IP address of my web server I get content and when I user something like this 111.111.111.11/~usernameofaccountthatdoesntshowup I get content.
This means that server is up and there is content for somedomain.com but it is just not shown.
Weird thing is that after few hours, it works and latter it does not. It just going on and off randomly.

I have 2 name servers that I did registered with domain on domain seller that I used (aitdomains.com)
Is that good thing?
How to fix my problem? Anyone
I am desperate.