This might be a simple issue of the meter not getting a good solid read. My Fluke 179 does this sometimes if I'm holding it against solder rather than the metal lead or an exposed bit of pad, or if there is any shakiness or wobble on the end of the probe (even barely perceptible - you'd be surprised how little play is required for the meter to get weird). However, let's leave this alone for now, because as you'll read below, it looks like we may have found our issue.
Okay, this would suggest that we have no short to ground, which is good, but also leaves us back at square one.
This is different than before. In previous tests, you said you had AC signal on the primary side of the transformer when injecting a test tone with the unit set to "IN." Now you do not?
EDIT: Ah, I see that in this post you took the AC measurement at the card connector - I misunderstood and thought that you confirmed that you had the same signal on the primary of the transformer. So you probably didn't have it then either.
If that's true, then
@capacitorless is right, the issue is on K1. Let's test both of the relays. Perform the following tests to confirm, after which (assuming these come out as I expect) we will probably just need to replace one or both of the relays:
Test 1:
-Power ON
-EQ BYPASSED
-Send test tone
-What AC voltage do you measure between In+ and In-?
-What AC voltage do you measure between Out+ and Out-?
Test 2:
-Power ON
-EQ IN
-Send test tone
-What AC voltage do you measure between In+ and In-? (It's fine if it's identical to the measurement from above)
-What AC voltage do you measure on the J1 connector between the second and third pins from the right?
-If you had voltage on those pins of J1, do you read the same voltage between Pins 2 & 5 of the transformer?
These first two tests should confirm whether we have a breakdown on K1. Now let's double check K2:
Test 3:
-Power ON
-EQ BYPASSED
-Do you measure continuity between "Or" pad of Output Transformer leads and "Out +" on edge connector?
Test 4:
-Power ON
-EQ IN
-Same question as in Test 3