have you recently upgraded your o.s. or been mucking about in bios...
if so go back to bios and make sure you load optimized defaults. and check the drive is showing up in the drive list.
if you were upgrading your o.s sometimes win7 and vista wont pick up the cdrom if the board is older.
your cd rom doesn't connect to pci-e it should connect to either the sata or ide block. with either a sata or molex power cable as well as an i/o cable.
if its ide the cable will be a ribbon type. make sure you have the cable the rite way round and there are no broken pins... you can tell which way it goes because there will be up to 3 connector blocks at the end that plugs into the drive and 2 nipples which will tell you which way up it goes. also connect the drive to the very last block. not doing so can fool the pc into thinking there is no drive attached to it on older systems. and dont forget that ide drives need a 4 pin molex connector for power... yeah i know but you would be surprised at how many forget or mistakenly plug in a 4 pin that only has 2 of the wires connected.
if the motherboard pin is broken then you will need to get a sata cd if the board supports it.
ide hard drives and cd-rom are keyd with one pin missing. http://www.gocomputertraining.com/what-is-hard-drive.ht...
ide drives have jumpers on them (master/slave/cs) you can have two ide devices on one cable. most older mb used to have two ide connectors..ide 0 and ide 1. most people used to put the cd-rom on ide1 by itself with the jumper set to master. newer mb will have one or no ide connector. if your mb only has one the jumper on the cd-rom drive needs to be set as slave if you connect it with another device or hard drive.