I noticed that the server with the wrong IP issue only has one DNS listed which is itself. On the other server that lists the correct IP for our site it has both IP addresses listed under DNS (itself and the other server that resolves our website's IP wrong). Should I add a second DNS entry on the problematic server? Would that have any chance of fixing the issue?

Good idea with the ipconfig /flushdns, but it doesn't work and the ping -a doesn't work either.