I just checked, and the correct expression is deep-seated, rather than deep-seeded.
No doubt the latter expression arises from a combination of folk etymology and phonetic 'laziness' (although, as my Oxford sociolinguistics tutor points out, 'laziness' is a term that should be discouraged, it being critical and often incorrect).
The correct phrase (deep-seated) was first used in it's figurative use in 1847, so it's not terribly old. However, the word it stems from - seated - is not commonly used these days in the way it's meant when it is referring to something that's ingrained and deeply-rooted (and doubtless this is where the confusion starts to arise). However, to seat not only implies, well, sitting...it also means that something is situated inside, firmly placed, planted, rooted...
And we come full-circle, both to the botanical and also to the image of something - an object, an idea - well and truly positioned and deposited in a certain locale.
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The term can also refer to one's position as being deeply ensconced in The Comfy Chair. :)
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