[Hmmm, I could have sworn I replied to this over the weekend, but it does not seem to be here....]
Anyway, there is a problem with setting commit-times to yes in the config file. The problem is that, while this is desirable for checkouts, it is not desirable for updates. Unfortunately, the option applies to both when set in the config file.
In our environment for developers, we suggest that they not set commit-times to yes in the config file, because updates should always set a newly updated file's timestamp to 'now' rather than the commit time of the file, thus forcing a rebuild. Instead, we use a wrapper script for checkout only, where the commit times are used for timestamps -- necessary for us, because certain packages should not redo any automake step, and when the timestamps are random, this sometimes happens.