I think that most people will consider "0.01" to be a newer release than "0.0.3". "0.01" reads as major release 0, minor release 1. "0.0.3" reads as major release 0, minor release 0, patch level 3. I don't think you should interpret Damian's suggestion to use three part version numbers as an invitation to just take your two part version number and insert an extra dot. I would consider "0.01" and "0.1.0" to be equivalent, and hence, "0.0.3" to be an older release.

Thanks for the insight.