D3 is actually toxic when present in large amounts, however in smaller amounts it helps the leo use the calcium it ingests.
In many other species, they make their own D3 using the UVA/UVB rays (I foget which one is responsible) that they absorb. Tthis is why a Green Iguana will develop MBD if not given proper lighting - it won't be able to produce D3 which in turn will not allow calcium to be used in the system, leading to soft bones and a list of other medical problems.
For these reasons, D3 is usually given with prey items to help the geckos use the calcium, but allowing the gecko to have unlimited (and unmonitored) access to it constantly presents the opportunity for the gecko to actually poison itself by ingesting too much.
Of course, there's not a whole lot of research on how much is "too much", so I'm just kind of going off of common practice.
Hope that helps clear up some confusion (or possibly make it worse... lol).
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Brian Skibinski
Brian@MilwaukeeReptiles.com
WYSIWYG 
