Moving to business
Did the agent actually wake up to take the new package? If the ports are different it might not have. Try downloading the installation executabel (Framepkg.exe) from the ePO server. Select "Create and download agent installation package"
That's worked for me in this type of scenario.
I think you may have more serious problems than you thought... the agent wakeup call port is not used for agent-to-server communication, so if the agent is installed but the machine does not appear in ePO, then agent-to-server communication itself must be failing.
Before anything else, check the agent log on the affected machine(s) - are there any errors related to communication?