Challenging Situation with IDE1 IDE2 and Optical Drives

I had setup my new build, which is in my sig. To start with, I just hooked up a cd-rom to install software with. After things started to shape up, I decided to hook up my dvd/rw on the same IDE channel as the CD-Rom was on. I inadvertantly had hooked these up to IDE 1 and had decided maybe they should be on IDE2. Well, I had a no boot situation at that point. I then just switched the optical drives cable back to IDE1 and all is well.
My question is, does it matter which IDE channel the CD-Rom and DVD\RW are on, as long as there are no other drives involved.
My Sata HD is on Sata1.
Just don't know if there would be any speed difference in the two choices??? 
Thanks for any input, advice. The machine seems to be running like turpentined Fox. 
Regards; Pop's

Answer 1: No, there shouldn't be a problem if they are connected to IDE1 or IDE 2
Answer 2: There will be no speed difference as both IDE1 and IDE2 provide same speed transfer
However I would hook them to IDE2. Certainly there would be no problem to be on IDE 1. I had this myself but MSI manual says "the first hard drive should always be connected to IDE1". They may as well mean optical drive, but when I had my DVD-RW on the Primary IDE channel, I had problems flashing it - carefully looking at it and I saw NEC reccomends that when flashing drive bios the drive needs to be master on the secondary IDE channel. I did it and I had no problems.
Now your windows had  the drivers for your drives installed and it may be looking for them on the original(IDE1) place of installation - and there you go - a problem.
Another version - you may try to reset bios or to allow bios to find the drives on their new position(IDE2). I had this problem also, but when I allowed the bios to find them - no problem afterwards. It's just your bios that remembers that there are drives on IDE1 and all of a sudden there is nothing there. I believe that this is most likely to resolve your problem.
Let me know if the above helps.
BTW I believe you set the jumpers to master and slave on the drives? And you have the correct bios settings like enabling IDE2 etc.

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