Well this is pretty strange, since there should be no reason for the speed to drop off.
Just out of curiousity, is UDMA enabled in both your H.D.D. and the Plex?
Do you have the Proper Chipset drivers relative to your Mothernoard installed ?
Are you using the 80 Pin IDE UDMA compatibile cables?
I know that you mentioned that Nero allows you to burn at 40X but as you know in Nero there is no indication during the burn that exactly what speed the burner starts at and at exactly what speed it finishes.
Have you tried the CD or Drive Speed in Nero to find out exactly what your Blank CD is capable of when its pushed to its limits?
Hve you tried a different media just to see if you observe a difference?
Although the speed measure in Clone is not a 100% accurate, I 'd be inclined to say its pretty close at least closer than what Nero reports.
Have you compared the timimng of the Burn ot your image using the similar settings in Nero and Clone, Protection wise speraking to see if there is a big gap timing wise?