I am not sure that this response actually makes sense.
If there was a general conflict between mootools more and bootstrap's use of jquery, then it would also be evident in the Protostar template too. But it isn't. So it is almost certainly something that the T3 framework does and so presumably it should be fixable.
I am still detecting, but one thing I have found is that T3 has the vanilla bootstrap.js from Twitter, but the Joomla 3.1.4 distro has some changes made to this in 4 places all to do with hiding stuff including the hide function for tooltips.
So, it looks like we should assume in \source\plg_system_t3\includes\core\template.php that the T3 bootstrap.js should only be included when version >= 3.0 and < 3.1.4.
I will see if this fixes things and if so, push a PR for this tomorrow.
Ok - I have fixed this - and the fields are no longer disappearing when the tooltip closes with my fix and Joomla 3.1.4.
I have created a PR-129 with this fix. But you need to update to Joomla 3.1.4 also - beware that 3.1.4 is very new and I know of at least one Joomla extension which needs a fix to work with 3.1.4.
I note that 4 weeks later and this fix has still not been merged - nor has anyone from joomlart even commented on it.
Having put the effort into identifying the issue, tracking down the cause and creating a fix, it would be nice if someone from joomlart had the courtesy at least to review and comment on it.
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