Just in case you haven't already solved this problem, let me offer the following guidance young grasshopper:
1st...don't combine HDD with CDrom on the same cable if you can at all avoid it. Put like devices on the same cable.
2nd...Put your primary and secondary HDD on the same EIDE cable in EIDE slot 1 (which should be labeled "PRIMARY EIDE"), and make sure that the cable is put in with the red stripe on pin 1 of the connector.
3rd...Make sure that the master (boot) HDD is on the first cable connector and the slave on the last and that the jumpers on the HDD's are properly configured for master and slave. You will have to look on the end (back) or on the top of the HDD for the jumper configuration. If it is not there, then go to the manufacturer's website and get it.
4th..,Put your CDrom's on the same cable and configure them the same as you did the HDD's but plugging into slot 2 (which should be labeled "SECONDARY EIDE"), and again make sure that the cable is put in with the red stripe on pin 1 of the connector.
5th...Make sure that your BIOS is set to "AUTO" on detecting storage devices and that when you boot up, you see all devices recognized.
To further test you system:
You should have system bootable floppies that load the CDrom driver(s). You can watch the boot up and verify that the CDrom driver's are detected and MSCDEX is loaded which allows your operating system to see the CRrom's.
Windows should autodetect all storage devices unless your jumpers or BIOS are configured wrong. If you still have a problem, try reinstalling windows or come back here for more opinions.
But just remember young grasshopper...opinions are like Adam Henry's...'cause everyone has one!
Live long and prosper, be kind to creatures smaller than you and most important of all...put the toilet seat back down when you are done ('cause that will allow you to live long and prosper)!
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