An updated search is performed for gluino, top squark, or bottom squark R-hadrons that have come to rest within the ATLAS calorimeter, and decay at some later time to hadronic jets and a neutralino, using 5.0 and 22:9 fb-1 of pp collisions at 7 and 8 TeV, respectively. Candidate decay events are triggered in selected empty bunch crossings of the LHC in order to remove pp collision backgrounds. Selections based on jet shape and muon system activity are applied to discriminate signal events from cosmic ray and beam-halo muon backgrounds. In the absence of an excess of events, improved limits are set on gluino, stop, and sbottom masses for different decays, lifetimes, and neutralino masses. With a neutralino of mass 100 GeV, the analysis excludes gluinos with mass below 832 GeV (with an expected lower limit of 731 GeV), for a gluino lifetime between 10 μs and 1000 s in the generic R-hadron model with equal branching ratios for decays to (formula presented) and (formula presented). Under the same assumptions for the neutralino mass and squark lifetime, top squarks and bottom squarks in the Regge R-hadron model are excluded with masses below 379 and 344 GeV, respectively.