It's a known problem that the older Bootstrap didn't work out of the box with jQuery UI, as you can see from this github discussion.
There are a few mashups of the two, including jQuery Bootstrap by John Seigers and jQuery UI Bootstrap by Addy Osmani.
Are those mashups still necessary with the new version of Bootstrap, or can you now just use Bootstrap and jQuery UI out of the box (as is alluded to vaguely in the github discussion)?
I am implementing a solution which is using Twitter Bootstrap 2.1 and jQuery UI 1.8.23 and I haven't experience any trouble so far.
Apparently Twitter Bootstrap v2 no longer conflicts with jquery ui.
You can find some more infos here.
Mark Otto states
We cannot guarantee compatibility with other frameworks like jQuery UI ...
so I guess you might have problems with some jQuery UI components and ask them to help you and find a solution.
At the moment I have a few problems with jqGrid.
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