priority-map-by is going to do funky things if your ordering function
does not obey the trichotomy property (i.e., for all a, b, exactly one
of a<b, a=b, or a>b holds).
The reason for this is that priority-map internally uses Clojure's
sorted-map, and Clojure's sorted-map does funky things if the ordering
function does not obey the trichotomy property.
Let's take a look at the behavior of Clojure's sorted-map with
something similar to what you are doing:
user=> (def s (sorted-map-by #(> (count %1) (count %2))))
#'user/s
user=> (def s1 (assoc s {1 3} 2)))
#'user/s1
user=> s1
{{1 3} 2}
user=> (assoc s1 {2 3} 3)
{{1 3} 3}
Look at what happens here. Clojure's sorted-map gets confused because
your ordering function suggests that {2 3} and {1 3} are considered
equal, so it just overwrites the value associated with {1 3}.
So since your comparator function screws with sorted-map, it also
gives bizarre results with priority-map-by.
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