Is this problem limited to one card reader, or is it happening with all 125 kHz readers installed in that spot?

Brian;

It's happening at one specific location.  Isolate that reader from the outdoor gate location it's in, and it goes away.

It could be the wiring path from reader to controller.  Wiegand D0/D1 wires get shorts or breaks and I've seen similar issues.

Can you verify the cabling between reader/controller in that spot?

I have seen this type of problem before. I would suggest exchanging the problem reader with another reader to see if the problem follows the reader or stays the same even with a different reader. Sometimes a specific reader will have a problem at one location but will work fine at another location 

I would also look to see if there is possibly cross-talk between the cabling going to the reader and other wiring that may be in the same conduit.

If the wire is going underground then the wire probably has some nicks in outer sheath and is basically shorting out. Is the wire plenum or is it either direct burial or water proof. Plenum cable starts acting like a sponge after being in water for a period of time. Then the the conductors start corroding as well. Since it is a prox reader there probably aren't any extra conductors on the pigtail. I have seen where an iclass type reader where the extra conductors weren't trimmed back cause issues as they were shorting out. 

Unmount the reader enough to place it in a Faraday bag, which is just an inexpensive mini version of a Faraday cage.

This will block any stray signal that could be interfering...

As you have tested the reader connected directly and it is fine my guess would be either interference or a bad cable. If it is on a metal post try isolating the reader with a piece of plastic or something similar. Also, grounding the shield in the cable could help as well. 

I have seen this before and it was interference caused by an exterior light located very close to the reader. If the misreads occur close to or at dusk and there is a light with ballast nearby, this could be the cause.

We build in HID readers embedded modules into our Handheld Badge readers and have seen ghost reads on numerous occasions - with no other 125KHz signals around.

These are the same modules that get used in many of their wall units.

We have fixed this by loading a stripped down configuration to the readers using configuration cards. Having more than one type of modulation (ASK/FSK/PSK) enabled seemed to be the culprit.

Maybe this will help you with your problem.

I've seen this occasionally over a period of several years. We called it "ghost  clockings". Could isolate some of the problems:

- readers too close to one another (Entry/exit situation)

- microprocessor controlled doorlocks too close to reader

- in some cases no cause was found and we replaced the standard 125kHz readers with Wiegand multi-discipline readers (i.e. 125kHz plus various 13,56 MHz protocols) provided one had used  a Wiegand i/f. This solved the problem.

Low Power at the Reader Head, Shielded on both ends (intentional or inadvertently - always ground only on the panel side and insulate at the demarcation point), unused pigtail wires insulated from each other and ground, RFID reader nearby (parking control for tagged vehicles). The key is are the bogus reads being offered up random non-existent credentials or is there a pattern? Are any parties using a dual-technology cards?

Probably either a lack of (1) an earth ground or, (2) a bum reader (these things happen).  From the description my suspicion is the system lacks of an earth ground.

Recommend tying the reader's cable shield drain wire directly at one point to the earth ground line.  The earth ground line should connected to a copper ground rod, or alternatively copper cold water pipes.  This will allow errant signals (i.e. EMI or 'noise') that make cause abnormal system operation to be drained off and minimized.

Here's a link from the past that may prove useful: http://www.farpointedata.com/downloads/pr/Grounding_Guide.pdf.

Good luck!

-Scott