I just noticed this yesterday so had to change my versioning system to avoid confusion later but not sure if you were aware of the lack of consistency.
An example:
http://www.wowinterface.com/download...Piel.html#info
Version Text: 7.03.00.735.26899 was allowed to be entered on the Update/Create screen. It shows correctly on the main page for the addon. However, on the Other Files page it is showing as 7.03.00.735.268 when the next update was made. Similarly the next version 7.03.00.735.26972 was showing as 7.03.00.735.269. Thankfully different enough to identify the version in case there was a need to roll back or test an earlier version for bugs etc. I then followed it with another update but where wow hadn't had an update itself it was the same version number but with .1 at the end to signify it was changed... realising it would be a problem I have had to adjust the version number to 7.3.5.26972.1 instead ignoring the 70300 prefix.
Like I said, not a major heartache to change the version numbers on the next update for my addons now that I know, but if this wasn't intended to be happening I thought it best to make it known.