you can minify bootstrap but a few rules:
Make sure you dont minify a minified version, Taking out the block comments /* */ seems to make things less buggy. and finally seperate everything out like so:
bundles.Add(new ScriptBundle("~/js/jquery").Include(
"~/assets/js/jquery-{version}.js",
"~/assets/js/jquery-migrate-{version}.js",
"~/assets/js/jquery.flexslider.js",
"~/assets/js/jquery.isotope.js",
"~/assets/js/jquery.fancybox-{version}.js"
));
bundles.Add(new ScriptBundle("~/js/bootstrap").Include(
"~/assets/js/bootstrap.js",
"~/assets/js/jquery.validate.unobtrusive-custom-for-bootstrap.js",
"~/assets/js/bootstrap-datepicker.js"
));
bundles.Add(new ScriptBundle("~/js/custom").Include(
"~/assets/js/revolution.custom.js",
"~/assets/js/custom.js"
));
I find that this method seems to calm the beast down and you get good results. i also find that:
<script src="~/assets/js/jquery.validate.min.js"></script>
<script src="~/assets/js/jquery.validate.unobtrusive.min.js"></script>
These file are best done on there own, and cause major issues with the script bundling.