It is definitely a good idea to upgrade to the current version. v5.0 was pretty buggy, still.
As for agora.cgi cloning itself... AgoraCart does NOT do that.
You may need to ask for evidence of what they are claiming agora.cgi is doing.
You need to check what all you have on the server. If you have any .php scripts they could be causing problems as they are easier to hack.
You should, also, check over the files to see if someone may have put a file in there that doesn't belong.
There is always the option of having someone that deals extensively with AgoraCart check over your server files and AgoraCart, itself.
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God Bless!
Bonnie - AgoraCart Moderator
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