The main site was victim once of a malware/trojan, but even if it didn't happen; because it's on a shared server; any other websites on that server could also have resulted in the server's IP being logged somewhere by Malware Bytes.
In my opinion IP based protection for surfing web sites is a bad solution, their lists are either out of date, or they are blindly punishing websites that share one server, something that is handled better by the warning that you get in Chrome and Firefox when accessing infected websites.