We have this issue too with other implementations of this template, see http://joomla.github.io/phpdoc-jdotorg/packages/Joomla.Libraries.html (I don't think we have anything on the developer site with this type of button use). So if there is a good fix for this, make sure I'm pointed to it so it can be applied universally.

The only fix here is to apply z-index: 3 to .subnav.affix class. Check the fix on my live demo. But it is BS related as I understand and do not know how this will affect other things. Should not in fact :)

This also happens on the "bootstrap switch"

I just removed z-index: 3 from my live demo. But it should help also in this case.

Well another way to fix it is to apply z-index:0 to

.btn-group > .btn:hover, .btn-group > .btn:focus, 
.btn-group > .btn:active, .btn-group > .btn.active

And also .has-switch label has z-index: 100. OMG 0_o Why that is needed for a "bootstrap switch"? Cmon...

UPDATE:
After digging a little bit more I found the solution that covers all ugly z-index things (see also #192) - applying z-index: 1020 to .subnav.affix.

Should we stay with it?

OMG 0_o Why that is needed for a "bootstrap switch"? Cmon...

Exactly! You shouldn't need to muck around with such crazy z-indexes. But, your updated solution sounds reasonable (I can't test ATM though), short of rewriting all of the z-indexes in Bootstrap.

@betweenbrain - I added you to have full access to the Joomla org on here now. You'll see a couple of private repos including the source files for this version of the j.org template. FWIW, it hasn't been touched yet for CMS 3.2 (but shouldn't need to I hope). If you can update that so everyone using it can update their sources with these fixes until we get it on a CDN, you'd be helping a lot of folks out.

OT but the dev site suffers from similar issues at certain resolutions

As does the API site. Hence my suggestion that if we get this fixed, we do it in our template so we're fixing all sites at once (or whenever their admins get around to updating).

@betweenbrain - I added you to have full access to the Joomla org on here now. You'll see a couple of private repos including the source files for this version of the j.org template. FWIW, it hasn't been touched yet for CMS 3.2 (but shouldn't need to I hope). If you can update that so everyone using it can update their sources with these fixes until we get it on a CDN, you'd be helping a lot of folks out.

Thanks @mbabker, I'll do my best. I'll create a branch and make a PR when I feel that I have something that helps.

all up @betweenbrain

After digging a little bit more I found the solution that covers all ugly z-index things (see also #192) - applying z-index: 1020 to .subnav.affix.

This does seem to fix the issue in the Joomla.org template. Thanks!

goes to me Will push changes also to our CSS then ;)