@User I got a clean LVS run last week on the same block with the same magic version. Maybe there's a difference in the GDS that's causing it. I don't know if it's relevant, but the feedback report on the run with errors has these lines.

box 104502 79709 104504 79711
feedback add "Label \"no_jumper_check\" attached to more than one unconnected node: c_83_258#" pale
box 104605 79709 104607 79711
feedback add "Label \"no_jumper_check\" attached to more than one unconnected node: c_186_258#" pale
box 104652 79694 104654 79696
feedback add "Label \"resistive_li1_ok\" attached to more than one unconnected node: c_233_273#" pale
box 104464 79694 104466 79696
feedback add "Label \"resistive_li1_ok\" attached to more than one unconnected node: c_45_273#" pale

Looks like it's a problem or incompatibility with the current GDS. This GDS extracts with no errors. (cksum)

1092943470 45638256 caravel/openlane/DFFRAM/runs/DFFRAM/results/magic/DFFRAM.gds

This one has the unconnected node errors.

3090695239 46588662 caravel/gds/DFFRAM.gds