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Running japgs update2 scripts with 1.3 software is a mistake. I know, I did the same thing to my 1.3 and got the exact symptoms you describe. A pity, because I had the original scripts working OK until I decided to grab the latest and greatest. "If it ain't broke...keep trying."

runupdate.tcl is different for the 2.0 libs, running it on 1.3 fails and seems to orphan some items in /MyGuide/Programs. Once that happens executing runupdate.tcl from the original update on jpags site just fails early into the listing and reboots Tivo just as your traces show. I tried to clear out /MyGuide as suggested by jpags but it didn't work. He has a script that might clear this data out that he is going to send me, if that doesn't work I will likely do a factory reset. I'd be surprised if that doesn't re-initialize MFS, but I hate to lose some dubbings I did.