OK.. So Rick, you make a lot of good points on what potential items to look at. I'd like to focus on two interesting items. First with Doug, when he went from the OSA rack to the 51x rack, his -4 when in went away. Second is on Robert's where he had his MOTU on both sides of the EQ and sees the same.
My testing environment here consists of Apogee converters and either a 51x rack or my bench setup which is the same thing just without the card cage. This is very similar to Robert's setup.
I've been sitting here trying every possible combination I can of reversed pins, disconnected pins, grounded/not, etc. The only somewhat interesting result I've had is that on the input side, if I float the low, the EQ magically makes -4.5db. Inside the 550, this is grounded via pin 5. If the low were not connected at all on the card edge, bypass wouldn't work. This tells me that the only way to float the low and see the results we have would be with a grounding issue.
Another note is that if in your rack, pin 5 were not connected to ground, there is a backup path to pin 13 via the 10R on the bottom rear of the board. If both were not connected, the unit wouldn't power on. So here's my wacky proposal - pin 5 doesn't go anywhere AND there's some problem with the 10R, then when EQ is in low would float and when in bypass, low in would connect to low out as normal.
That's a REAL stretch but, it does seem to fit the symptoms anyway and causes the same result. Robert or Doug, could I ask you guys to do a very quick test for me? With the unit out of the rack, check DCR from 5 to 13. Should read 10R. If that's an open, then see if pin 5 in your rack goes anywhere.
So then if all these crazy IFs line up, then we roll back to Rick's question about some commonality of what might be interfacing the device's input and maybe actually draw a conclusion. Of course if it's a grounding problem like that, the conclusion may be that the design of the thing is just inherently not tolerant to these sorts of issues. That's a nice way of saying I could have done it better