2nd Hard Drive Problems

Help!
My set up is as follows:-
IDE 1
Master: Seagate ST3120022A 120Gb 7200rpm
Secondary: Liteon 16x48 IDE DVD-ROM DRIVE
IDE 2
Master: Pioneer DVR-106 4x DVD DUAL R/RW
Secondary: Liteon Western Digital Caviar 80gb 7200rpm
When I scan disk with Norton at the end it says I have 2 boot sectors.
Also if I try convert AVI to DVD the sytem freezes. this is with Easy CD, NeroVission Express Tmpeg (to many to list)
After many hours and trial and error I have found that when my second hard drive is not connected.  I have no problems burning, converting AVI to dvd etc.  When I scan the disk with norton it say it has only 1 boot sector.
I have checked my jumpers on the hard drive etc all set correct.
I have also swaped the hard drives round (the 80Gb as the sytem) but I get the same.
Can I not have a second hard drive on my computer?
Many thanks in anticapation.
Homer
MSI K7N2 Delta-L SKT A 8xAGP DDR400 Nforce2
Arctic Cooling Copper Silent 2 Tc
Tyan Tachyon Radeon G9600PRO 8xAGP 128MB DDR
AMD ATHLON XP2700+ 333MHZ FSB 256Cache CPU
Samsung 512mb PC3200 400MHz DDR Original
Crucial 512 DDR333 PC2700 DIMM
Western Digital Caviar 80gb 7200rpm Ide  
Seagate ST3120022A 120Gb 7200rpm
ATX Midi Tower 350w
+3.3V = 28a
+5V = 35a
+16a = 17a
Windows XP Home SP1
Pioneer DVR-106 4x DVD DUAL R/RW IDE BURNER
Liteon 16x48 IDE DVD-ROM DRIVE

I usually run both hard drives on IDE 1 as cable select. Or as master/slave. Then leave the opticals on IDE 2.

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