Two very different results using the same settings (H.264 / Quicktime Pro)

I’m a bit confused, I have used Quicktime Pro (v7.1) to encode DV into H.264 for iPod and this particular video is 18 minutes long and came out looking very good with the following settings;
VIDEO: H.264 at 200kbps, Baseline Profile, 25fps, Auto Key Frames, 320x240 or 640x480, Multipass Best quality encoding.
AUDIO: AAC Audio at 96kbps, 24kHz sampling freq, Stereo.
However here is the twist…
When I use the same exact settings to encode just the 30 second opener (from the 18 minute video) the encoded opener looks bad and blocky!
Why? Same settings would make you assume that you should get a same or similar result, or am I wrong?
The reason I have tried encoding this 30 second opener is that I am trying to work out which settings work best on the iPod (another issue) and I don’t want to spend hours test encoding the full 18 minute video, as you know H.264 is SLOW to encode!
So can anyone help in regard to two very different results using the same settings?
Regards,
J
PC   Windows XP  

Alvin,
Is it a commercially-released or home-burned CD?
If it's commercially-released, try "encouraging" the recalcitrant computer by using the iTunes Advanced menu > Get CD Track Names command when it shows Audio CD.
If it's home-burned, you will find that only the computer that actually burned the disc will know what's on it. The information won't be transferred to another computer.
Let us know which, if either, of these situations applies to you.

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