Result I get in Clozure 1.4 on Win32:
? (find-symbol "PROCESS-RUN-FUNCTION")
PROCESS-RUN-FUNCTION
:INHERITED
? (symbol-package *)
#<Package "CCL">
Make sure you use "PROCESS-RUN-FUNCTION" when searching, as it searches for the symbol name, which will be upcase depending on the readtable that was used when reading said system library code. Disregard what I said if you actually recompiled CCL with readtable-case equal to something other than :upcase.
One more thing, features like threading are usually too fundamental to disappear at runtime, they're usually determined at compile-time. Check your *features*.