This came in on the mailing list: https://mail.openjdk.org/pipermail/shenandoah-dev/2025-December/028724.html.

Summary:
I believe the issue is a Reference in the old generation will sometimes fail to be discovered by the GC. A reference in the old gen will not be encountered by any young gen collections. And when it gets encountered in the old gen, should_discover() is returning false, so there's no way for it to ever be enqueued. I think this is due to the references being wrongly considered strongly live:

[23.999s][trace][gc,ref ] GC(259) Encountered Reference: 0x000000030000b6e8 (Weak, OLD)
[23.999s][trace][gc,ref ] GC(259) Reference strongly live: 0x000000030000b6e8