Here's what I got from the PAUSE indexer report. A status of "Falling revision number". The Indexer was somehow converting "0.0.3" to "0.000003", and that being less than "0.01", hence the error.
While I think that converting "0.0.3" to "0.000003" isn't the correct way (and the PAUSE indexer contains more 'surprises', for instance, it thinks that "0.2" is a newer version than "0.11", because it considers "0.2" to be a short hand for "0.002" and "0.11" a short hand for "0.011" - not that this is an idea of PAUSE - Andreas is just doing what perl is doing itself), 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.
I suggest you keep 0.01 in your CPAN dir, and name your new release "0.1.3", or "0.2.3", and count from there.
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