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Under versions detail, 3.1 is after 3.03.
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The PHP function in the VanillaAddons site that is providing the sort order is version_compare. This function splits on periods (and underscores and hyphens and plus signs) and then compares each part from left to right. So from your example:
3 == 3
1 < 03
In your mind, it may seem like 3.03 is equivalent to 3.0.3 and 3.1 is equivalent to 3.1.0 but the former scheme is non-standard and ambiguous whereas the latter is well-understood and common.
See Also: http://semver.org/
Thanks for the example. Unfortunately, I still did not get your example.