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J-micron question

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ok i built a computer, i set up the two 1tb sata 3g harddrives on the jmicron ports and the disk drives in normal sata slots. Before installing windows on one of the 1tb disk drives i forgot the set the speed or setting for j-micron.After installing windows, only one hard drive showed up in my computer.I tried to set the state fo j-micron and it said it had to be formatted to do so or risk erasing, so i figured i would forget j-micron and just plug them into regular sata ports. I did this and both 1tb drives show up in bios but not in windows under my computer.I also have an external 500gig, and an old 500gig IDE showing in both bios and my computer, but the second 1tb drive will not show, any help would be appreciated, emailformark@gmail.com

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Yes they were both brand new out of the box. the external was not, and the internal 500G was not, but those show up,only 1 of the 1g drives show up under my computer, they both show up under device manager. The drive were originally plugged into the two orange J-Micron slots, but after i installed windows 7 and realized i was supposed to set the j-micron settings under bios prior to putting anything on the hard drives, it said if i adjusted the settings after installation that it would risk erasing everything.I bought the OEM copy of windows 7 pro 64 bit from new egg so im not sure if i can reinstall it and start over, id rather not if i do not have to. At that time both drives were recognized in bios, i moved them both to regular sata ports to avoid the whole j-micron set up all together.NOw just the main one with windows shows up under my computer. Id really like to figure this out, I am much more of a hardware guy than a software guy.thanks guys.
 
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