I believe that this issue is related to the following improvement record:
Also, since this is a system feild, it seems to be a hard coded item and I can't see an option to do it. Anyway, I'd suggest raise a new support ticket at Atlassian Support or to a new improvement request at https://jira.atlassian.com
One way would be modifying the versions-edit.vm file (WEB-INF\classes\templates\jira\issue\field)
There is a #foreach loop that iterates through versions, you can reverse it by doing something like this:
#foreach ($version2 in $versions) #set($index = $versions.size() - $velocityCount) #set($version = $versions.get($index))
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