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Reflashing a BIOS from Windows

Beforing putting debian on an Acer Aspire 1690 that I inherited, I decided to reflash the BIOS to the latest version (the new one dates March 1st 2006 --- whippee!) figuring that would give me the best chance of success in putting this thing to sleep and having it wake up again. I have never had a great deal of luck doing this but one can only hope. To reflash the BIOS I downloaded a windows bios flash programme from the Acer web site that came with a whole raft of dire warnings but I plunged ahead anyhow. The reflash itself went painlessly complete with a back-up of the old BIOS and a compatibility check so I was reasonably happy that I wouldn't brick my computer but I hadn't reckoned on Windows freexing up solid not letting me shut down the machine. It was working as anice room heater and nightlight but little else. I started to sweat a little when holding down the power button did nothing at all --- this is a BIOS override of the OS and it wasn't doing anything at all! So I pulled the wall power, flipped it over and pulled the battery. It started just fine from then on. One presumes that Windows had deep tenticles into the BIOS and was expecting different behaviour from the reflashed version, which makes one wonder why write a reflash programme in windows at all? Does this make sense to anyone?