I'm assuming it's because the relationship calculator can only show one blood kinship at a time (in addition to only one in-law kinship, which it doesn't show at all in this case).
I don't know why it wouldn't default to the nearest blood kinship, unless only because it is so obvious that she is his mother.
Not so obvious that she is (allegedly) also his 5th cousin 2x removed.
The problem may (hypothetically) be somewhere in the lineage, rather than the fault of the software program.