I don't believe this is PG's fault. I can reproduce problems in tty mode. With the previous version, you sent C-c C-c and it reliably interrupted and printed "*** Interrupted". With Isabelle2009 interrupts may get ignored or go unreported and output and the following prompt may or may not appear.
http://proofgeneral.inf.ed.ac.uk/trac/ticket/179 I've added some workaround but it's not easy to tell between a busy prover and one that's been interrupted and stopped sending output but is too secretive to tell you about it! - David -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
