This is due to our keyboard input functions ignoring input when a form control is focused. Currently the 'check all' box unfocuses itself every click. It's possible to do the same thing with list checkboxes (just a bit messy).
I could also investigate allowing keyboard input when checkboxes are selected since the only real input they accept is the spacebar (not a hotkey we'd use).
http://www.cerb4.com/forums/showpost.php?p=9479&postcount=3
gentlemans01 in the forums discovered that keyboard shortcuts stopped working from the Overview and Workflow ticket lists. Long story short, it turns out he was stumbling on this old issue in JIRA. He threw this idea out there in case we ever decide to tackle this potential annoyance.
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I don't know if this is possible, but maybe instead of making all the checkbox controls defocus themselves after being clicked, (messy, per Jeff Standen's JIRA comment,) you could put a transparent graphic "cover" over the top of the checkbox so the checkbox itself never is actually focused?
the user can already click anywhere else on the row to trigger the selection, so the checkbox is really just window dressing anyway...
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