1. I don't understand why you're upset.
2. I don't understand why you'r crazy.
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Are both similar in meaning?
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3. I pased you message on to my mother.
4. I pased you message to my mother.
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Are both the same? What is the meaning of 'on' in #3? Do we have to use 'on'?
1 and 2 are not similar except for the main clause. The subordinate clauses are quite different in meaning!
For 3 and 4, I think you meant to write these:
3. I passed your message on to my mother.
4. I passed your message to my mother.
Both are correct, and they mean the same thing. You can use "on" if you wish, but you don't have to.