Most of the 55-GFR drives have a 1K SIP resistor pack permanently soldered into each drive. Termination is not what you were up against.
In making a first guess, I'd say your two drives are aligned slightly different. I assume you wrote the disks using the original drive 0? Drive 1, with a slightly different alignment, may have a hard time reading disks written by drive 0. Until the FDC+ has spun a few revolutions of drive 1 to establish timing parameters unique to drive 1, it has to use nominal values for timing. However, the first mount attempt on drive 1 has already failed by the time the FDC+ has gathered data for the drive. By the second time you try it, the mount works because the FDC+ has made a slight adjustment for drive 1's timing that is just enough adjustment to allow it to read the disks.
Here's an experiment:
1) restore the original configuration and duplicate the failure.
2) use PC2FLOP to write the disk image you're using in drive 1, but this time, actually use drive 1 to write the disk.
3) re-run the test of step 1 and see if the problem changes
Mike