Hmmm. Just had my A3000 apart. I'm running the 3640 in mine and it has always worked ok. But as I recall, there were about 3 or so jumper settings that had to be made on the motherboard and they did have to do with timing differences when using the 3640. There was also Buster rev11 (min rev9, I think) for it to work, and one other chip (Gary maybe??) that had to be Rev 7. This is probably the root of all your problems. I remember specifically that I had to change timing jumpers on the motherboard though.
Mine problems now are worse. I just got the thing connected to the broadband cable connection earlier today and it worked great. I had a couple of lockups with sucessful reboots. Then it quit booting at all. Just a black screen. The monitor gets a sync light, but it never attempts to boot (no hd led activity). A CTRL+A+A will reset as the hd reinits, but still a black screen and no attempt of disk activity. I've gone all the way down to the mainboard reseating everything about 3 times....I think something in mine has finally died. :-(