These tests have been written to use fn:doc rather than using an $input-context variable, which places an unnecessary reliance on URI resolution behaviour in the test harness.  The catalog is actually correctly setting $input-context, so the queries should probably have been written as:

(: Name: Catalog001 :)
(: Description: test all input files have variable references :)

(: insert-start :)
(: declare variable $input-context external; :)
(: insert-end :)

<missing-variable>{
  for $x in $input-context//*:input-file
    [count(@variable) = 0 and ./text() != "emptydoc"]
  return string($x/../@name)
}</missing-variable>

rather than using doc("../../../XQFTTSCatalog.xml")

Compare with the corresponding tests in XQTS.