This is because when I installed A, it set it's top folder to something like C:\Program Files\Ipswitch\WS_FTP Server\hostA.foo.com\, and when I installed B, it's folder was set to C:\Program Files\Ipswitch\WS_FTP Server\hostB.foo.com\ . Since I'm using the web front end to manage A, when I switch to manage B, the second directory does not exist.

This can be circumvented by simply changing the location to be a directory that exists on both servers, for example D:\iFtpSvcRoot or something.