Dialing in RAM can be tricky and can give you erroneous problems that can send you off in all different directions. memtest34 is great for RAM. (google "memtest34") PSUs are a squirelly lot and can also cause some grief if not properly selected and installed.
Viruses can do all sorts of fun things ot a computer. By their very nature they are designed to make you nuts. Screwing your MBR is just one of some of their lovely tricks.
A cable select cable runs pin 28 from mobo ground to the Master connector, only. The Slave connector has pin 28 open or ungrounded. This is how the drives configure themselves as Master or Slave. Having any other configuration (M/S drives on a C/S cable) is asking for trouble. Pin 39 on an non-C/S cable runs DA/SP (Drive Active, Slave Present) through pin 39 to both drives -which checks for an active drive and whether there is a slave present (all determined by the jumpers on drives). Having any other configuration (C/S drives on a M/S cable) is asking for trouble. The links I gave you explain this but they do fall short of outright saying it won't work, but it's clearly not how they're designed to work.
If the opticals were jumpered to C/S and they worked, they must have been on a C/S cable. If you inadvertently switched that cable to the HDDs and they were jumpered M/S they should not have worked (or, if you happened to put the drive jumpered to master on the master connector, you might have gotten lucky). If you subsequently switched that cable back to the opticals without changing their jumper settings (left them on C/S) and put the proper cable on the HDDs (a non-C/S cable), it should have worked.
SATA and IDE share the same ATA bus/channel on some mobos. -So, you might see SATA 1 & 2 and IDE 1 & 2 on the same disk controller in your BIOS. Whether one "kick-starts" the other is beyond me, but it sure doesn't make sense, and in fact I never heard of such thing in my A+ class.
But, bottom line, if you're up & running, great! What's the magic word? "Document!"
(sick of me saying that, yet?!?!)
