I have seen exactly the same behaviour with the last couple of Sneaky Peeks, and I think it has to do with sites using JavaScript to set the keyboard focus for form fields after they've loaded (though I must say I haven't looked into it so I have no evidence for that claim :)).
I particularly notice this with the UK National Rail site at
http://www.nationalrail.co.uk/. If I do a timetable search, then command-click one of the result links so it opens in a background tab, that tab grabs the focus when it finishes loading.
As the original poster described, the tab drawer exhibits some unusual behaviour in this situation, with the originally-selected tab retaining the outline of its 'highlight colour' around the tab thumbnail, while the newly-opened tab has its thumbnail indicated with the highlight colour as though it has been clicked. (Er, that description sounds a bit confusing, but short of a screenshot it's a bit tricky to describe...)