I don't know whether this is a know problem.
In a pdump xemacs command line flags like '-debug_paths' don't work.
If '-debug-paths' is present on the command line then the C variable
debug_paths is set to 1. To make it accessible to lisp it is
DEFVAR_BOOL'd, alas this also means it is dumped and thus restored
when the dump file is loaded.
A similar problems exists for '-no-early-packages' and
'-no-autoloads'.
Gunnar