optical disk problem

First of all , let me describe my configuration . I have two similar hard disks ( ST3160215A ) and two optical disks ( ASUS and TOSHIBA ) . The first pair (ST3160215A ATA , ASUS ) is on IDE of the motherboard ( Asus mobo ) and the second one in on Silicon Image Sil0680 ATA/133 PCI-2 IDE Controller (Driver version:1.2.30.1 , Flash BIOS :3.4.00 for Windows 7 from Silicon Support site ) . The second pair appears on Device Manager as SCSI . Now , the second hard disk D: is used only for back up purposes . So , using the Acronis True Image program create a clone disk of C: on D: ( in case of virus attack or windows problems generally ) . In the past , I have used the Disk D: , twice , in the place of C: and vice versus to overcome problems . The point is , this configuration , creates some problems in Windows booting and the optical disk ( slave on D: ) dissapears from My Computer no matter is playing ( a CD ) or is Idle . I have used the Repair Startup of Windows 7 DVD but the problem remains. I'm suspecting that the problem comes from the fact the hard disk D: is D: as hardware and C: as software and this might create booting problems in Windows 7 ( someone told me for Allocation Table etc ) . In case of changing the hard disks the D: becomes C: and has no problem at all in booting and windows operation with the the D: ( the previous C: ) disconnected . I need to make several restarts to force Windows to recognise the second pair ( SCSI ) but the problem with optical disk remains .It dissapears after 15 - 20 minutes approximately. Any help ?

my last view in this problem led me in the following conclusion : the whole thing is due to " Checknow " operation , which doesn't " understand " the configuration ( hard disk D: , is D: as hardware and C: as software ) and causes problems in booting files attempting to "correct" them . I stopped using Checknow and the problem seems so far to have been solved . Thanks anyway ! ! !