I've done a bit more testing. The slowdown happens if I only modify 1 Makefile.am, and it seems to be related to using SUBDIRS inside an AM_CONDITIONAL.
If I change the Makefile.am to use a non-SUBDIRS variable inside the conditional autmake zips right along. In fact, if I specify an as-yet non-existent directory to SUBDIRS I get a warning message out of automake. This surprised me - I thought I read that automake did not pay attention to SUBDIRS and got its information from configure.{ac,in}. Any ideas (while I go back to digging)? H