Further debugging showed that the original bug report was flawed.

The problem was actually caused by
https://issues.opendnssec.org/browse/OPENDNSSEC-285

The bug has been fixed upstream in 1.3.10.

The following patch applies cleanly to 1.3.9-5 of current stable 
release.

--- a/signer/src/signer/signconf.c      2014-05-08 12:58:54.000000000 +0300
+++ b/signer/src/signer/signconf.c      2014-05-08 12:59:12.000000000 +0300
@@ -179,7 +179,7 @@
     st_mtime = ods_file_lastmodified(scfile);
     if (st_mtime <= last_modified) {
         ods_log_deeebug("[%s] file %s not modified since (file %u, "
-            "mem %u)", sc_str, (unsigned) st_mtime,
+            "mem %u)", sc_str, scfile, (unsigned) st_mtime,
             (unsigned) last_modified);
         return ODS_STATUS_UNCHANGED;
     }   


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