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While I was eating is an adverbial phrase which tells the reader when the cat scratched. When you put this phrase at the beginning of the sentence, we don't know yet which verb it is describing (scratched). Therefore, we use the comma as a kind of visual trigger saying that it does describe something and you'll see what that is in just a second when you finish the sentence.
When you put it after the sentence, we already know the main thought of the sentence and can determine easily enough for ourselves what the adverbial phrase is describing.
Also, if you put it before the rest of the sentence, it starts to look like you're eating the cat.
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