I looked in the PLAYLIST folders on the disc itself and there actually WAS a 541 mpls. Why didn't MakeMKV show it in the list? Is this some sort of bug, possibly?
EDIT: I found the problem -- in MakeMKV messages pane after the disc was loaded I discovered the following:
Something to look out for. Anyway, the segment map for Amazon retail (244 mpls) is:Title 00541.mpls is equal to title 00244.mpls and was skipped
504 511 514 509 506 510 515 507 501 508 512 505 503 513 502