Trouble probing 1Vpp signal from Heidenhain LS403 with oscilloscope

Yes, a missing power supply may be the issue
All 7I77 encoder circuitry is 5V, so you would
need a separate 12V supply.

Do you have the converter manual? it should show
the 12V connection.
 

Yes, the missing power supply was the issue. I was being too careful in my attempt not to blow up the Heidehain cards, but now it works.

I have hooked up all three encoders and for the first time I can see some movement in the LinuxCNC UI.

Thanks for your help again.

The 0V, 5V and 12V pins highlighted look like test points to me. I wouldn't expect them to be scattered about the board like that if they were power inputs.

As for as I know Heidenhain LS403 is a 11uA signal . Not 1Vpp.
Please check the datasheet