The problem you found sounds like a mismatch of terminating hardware. You may have a 568A patch panel at one end and a 568B patch panel at the other end. You should be able to determine the pinout of the panels by examining them closely for manufacturer's markings.
You don't need to do anything to make a compatibale cable. A standard straight through patch cord with RJ-45 modular plugs on each end will work just fine. RJ-48 jacks have a shorting bar that creates a loopback when the patch cord is removed. This is a troubleshooting used by the service...
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