I have developed a hypothesis, which could explain eventually this strange phenomenon:
spamassassin reads the configuration files directly, but not spamd --- during installation the rules were compiled by the Debian postinstall script into a format, which is read exclusively by spamd during launch, ignoring all changes to the configuration files without recompiling them. (that seems to me the only logical explanation, so don't laugh, if this sounds really strange)
Untrue.
Everytime it launches, spamd reads the same set of standard numbered CF files and local.cf as spamassassin.
HOWEVER, it only reads them when it launches, not once per email. If you change these files you MUST restart spamd. (You might be able to send it a HUP signal.. I forget if spamd supports that or not)
The only file spamd reads on a per-email basis is user_prefs. (also, by default rules in user_prefs will be ignored and only score statements and various threshold/tagging options will be honored)
Also, I'd advise in general not editing the standard numbered .cf files, although trying it as a debugging measure is reasonable in your case.
Try a spamassassin --lint to make sure your files are syntax-error free.
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