Yes, i also had problems with this chip, i remember i was fixing this in 2 or 3 releases, but somebody tested it in real life and wrote that everything works ok. If fuse doctor reads signature properly, you can be sure its there and its ok. ISP software can be bugged and not tested with this chip. Try to use some newer software, try to download newer avrdude and read it trough line command instead GUI – because this also can be bugged. I’m not saying that fuse doctor is bug free, but breaking signature or changing it is „impossible” according to atmel. But i know that even regular ISP programmer can mess up signature bytes.
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