Firefox, AudioHijack Pro, MP3 Trimmer, iTunes and then iPod

I record a fair number of on-line radio programmes using Firefox as the browser and AudioHijack Pro as the recorder.
I then edit the recording using MP3 Trimmer, topping and tailing the programme to get rid of the extra five minutes at each end which I record incase the programme doesn't run precisely to schedule..
I then add the edited version to my iPod.
So far, so good.
But …
… the iPod version behaves oddly.
If I skim forwards through any of it, using the click wheel, the "end time" doesn't move, as expected. so when I start playing it again, when it reaches the time shown, it stops even though there is still some recording there - specifically the amount by which I "fast forwarded". This does not happen when I do the same thing in iTunes itself.
And boy does it annoy me!
So, something in the editing seems to cause the iPod to get its undergarments in a tangle – but what and why?
Does top and tailing remove some form of "timing" markers laid down by AudioHiJack Pro, or does it indicate something else is going wrong?
I hope that makes some sort of sense, because it's a tad difficult to explain!
Firefox v 3.6.8, Audio HiJack Pro, v2.9.6, MP3 Trimmer v2.9.4, iTunes v9.2.1 (4), 30GB Video iPod software v1.3, Kicked Passing Cat v1861.

WOW!! Thanks Meg St.Clair
I feel stupid, but at this point I'm just ignorant. Ya see, I'm an old Windows person, thus I think everything should be hard.
Craig

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