Master Server gets confused.

For some reason, when I try to have two servers going off of the same host (My VPS), the Master Server (Or perhaps SRB2) gets confused, and only hosts one of them at a time. In addition, I can't get details about them from the Master Server. I'm unsure if it's SRB2's fault or the MS's fault.

I remember such thing in SRB2. Tiley had that too when tried to host two servers off the same IP address, but from different ports. MS shows only one server from one IP at a time.
People can still join your server on another port using command
connect "<ip>:<port>"