Have you been looking at the output from running make -n and make -np, and the biggie make -nd?
Are you using a fairly recent version of gmake?
Have you looked at the free chapter on Debugging Makefiles available on O'Reilly's site for their excellent book "Managing Projects with GNU Make" (Amazon Link).
remake is a patched and modernized version of GNU make utility that adds improved error reporting, the ability to trace execution in a comprehensible way, and a debugger.
It has gdb-like interface and is supported by mdb-mode in (x)emacs which means breakponts, watches etc. And there's DDD if you don't like (x)emacs
-n, --just-print, --dry-run, --recon
Print the commands that would be executed, but do not execute them.
-d Print debugging information in addition to normal processing.
The debugging information says
which files are being considered for remaking,
which file-times are being compared and with what results,
which files actually need to be remade,
which implicit rules are considered and which are applied---
everything interesting about how make decides what to do.
--debug[=FLAGS] Print debugging information in addition to normal processing.
If the FLAGS are omitted, then the behaviour is the same as if -d was specified.
FLAGS may be:
'a' for all debugging output same as using -d,
'b' for basic debugging,
'v' for more verbose basic debugging,
'i' for showing implicit rules,
'j' for details on invocation of commands, and
'm' for debugging while remaking makefiles.
There is a GNU make debugger project at http://gmd.sf.net which looks quite useful. The main feature supported by gmd is breakpointing, which may be more useful than stepping. To use this, you download gmd from http://gmd.sf.net and gmsl from http://gmsl.sf.net, and do an 'include gmd' in your makefile.