[64 bit] IDE - SATA Incompatibility?

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http://ubuntuforums.org – I have recently purchased a new system. I have 3 problems which all seem to point to some sort of incompatibility between IDE and SATA drives. I'm probably wrong here, but in my mind I'm convinced that they are connected. I have a Foxconn A88GMV motherboard with an AMD Phenom II X4 965 processor and 4GB memory. The SATA is 1TB and the IDEs are 500 and 300MB. First I replicated my old system with Ubuntu 11.10 (now 64 bit and not 32) and Windows XP both installed on the SATA drive which is the master boot disc. I don't have any other issues in using the IDE and SATA drives - they mount and are (Hardware)