Maybe pop some incandescents in there before testing. Can't LEDs also ghost in test mode?

Here is the section from Clay's guide regarding two lamps on instead of one. This is what is happening, right?

Two Lamps On Instead of One.
If a lamp diode is shorted on (or installed incorrectly), this can cause two lamps to act as one. This can be seen in the "Single Lamp Test". Each individual lamp in the lamp matrix (as displayed on the screen) should flash. The "start game" button will move the test from one lamp to another. If TWO lamps flash in this test instead of just one, suspect this lamp has a bad or mis-installed lamp diode.

Testing a Lamp Diode.
In order to test a lamp diode, use your DMM set to diode test. Turn the game off and put the black test lead on the banded side of the diode. You should get a reading of .4 to .6 volts. Reverse the leads and put the red lead on the banded side of the diode. You should get a null reading. Any other reading and this lamp's 1N4004 diode should be replaced. You don't have to remove the light bulb or desolder the diode to perform this test. You can also test the diode soldered to the circuit boards that hold the 555 lamps in the same manner.

PM me if you need the entire document, it goes into detail on how to test each lamp at the board level to try and isolate the issue to the board or the play field.

Also from Clay's guide, general common issues with System 11 lamps:

Most Common Problems with Lamps.

Bad bulb. Any light bulb can burn out. Often you can visually see the bulb is burnt, but sometimes you can't. Test the bulb with your DMM, set to continuity. Put your test leads on the bulb. No continuity, and the bulb is bad.

Wire broken away from the socket. This happens quite often and requires re-soldering the wire back to the socket lug.

Diode broken away from the socket. If the lamp diode becomes disconnected from its socket, the lamp will not light.

Corroded or Bad Socket. Games imported back into the US from other countries exhibit this problem more often. Re-seating the bulb in its socket often fixes this problem. On 555 plug-in sockets, bend the contact tabs slightly for better contact.

Blown Fuse. If several GI lights don't work, check the fuse associated with them. If all the CPU controlled lamps don't work, check the fuse by the BIG 30,000 mfd capacitor and bridge bolted to the back of the backbox.

Burned Connector on the power supply or interconnect board. This happens most often with GI (general illumination) lamps. See Burnt GI Connectors for more info.

Lamp matrix power resistors. On the CPU board, lower right corner, there are eight .4 ohm, 3 watt wire wound sand resistors (R113, R116, R119, R122, R125, R128, R131, R134). Sometimes these resistors get hot and de-solder themselves from the CPU board and fall off (or the solder joints need re-soldered).

Bad Column Transistor. The TIP42 transistors that control the lamp matrix columns often fail. If this is the case, all the lamps in a particular column will be brightly locked on.

Two Lamps act as One. If a lamp diode has a shorted on, this can cause two different lamps to act as one.

Check those diodes. I think you can test them in circuit, correct? Very easy to do and quick.