IRQ handling is broken and not to be trusted in the current Jessie 3.16 kernel :-(
Please file a bug report. People will need further details to track it down.
FWIW, the latest 3.18 longterm kernel from kernel.org fixed all IRQ issues I was experiencing in Jessie's 3.16 kernel. I didn't try the latest 3.16-ckt kernel from the Canonical kernel team (which is the upstream of Jessie's kernel), though.
--
"One disk to rule them all, One disk to find them. One disk to bring
them all and in the darkness grind them. In the Land of Redmond
where the shadows lie." -- The Silicon Valley Tarot
Henrique de Moraes Holschuh <hmh@debian.org>