Just curious, and sorry if this sounds silly...
1) Have you tried "Scan for hardware changes" in device manager? (Right-click the name of your computer at the top)
2) Have you tried to see if this generic dvd-rom works on it's own, without the 3500 in the same channel?
3) Does this dvd-rom work with another hard drive / optical drive other than 3500 in the same channel?
4) Have you tried Nero Infotool and see what the configuration tab says?
It works by itself and it works when I put it as secondary on the cable when there are two drives connected.
I take it you mean the master doesn't work in this situation then? Does this only include the dvd-rom as the master or does this statement apply to some other drive when installed as master as well?