Now - keeping in mind that you might not want to SEE the the padded version, you might be able to create a calculated field that "pads" your number sequence like I mentioned. So - the user types in "1.2.3.4" and the calculated field would then have "001.002.003.004".
You can then order by the calculated field (make it persisted and put an index on it too).
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Your lack of planning does not constitute an emergency on my part...unless you're my manager...or a director and above...or a really loud-spoken end-user..All right - what was my emergency again?