May I suggest that we start with knowing the IP addresses that are assigned to you. If you don't know, submit a support ticket to your host asking that question. Be sure to ask what IP's are usable of the assigned group.
Once you have that information, you need to put on your detective hat. Start with putting the IP's in a browser. You should be able to determine how they are being used and then by whom. There are many on-line tools that will help discover & define their usage. Port scan the IP; get a domain name and do a whois; what ever; let the snoop come out in you! I know you have it, cause you are an admitted programmer.
My guess is that your host has bound 2 IP's to your server as posted. One is called the lead IP and is likely the IP that you are using on your current website. The second is then used to interface to a VLAN within the data center that allows background routing of all other assigned IP's to this single IP on your server. (This cuts down on the cost of the network infrastructure for the data center)
Depending on how well the background networking is configured, it is possible that someone has hi-jacked your IP's. This may account for the hosting company's response to your initial IP question. If the IP's are really in use and you can show an example of abuse by another client of the hosting company, that should spur them to take action.
Hope this helps.