How come thaw and unthaw mean the same thing?

Answer 1

While the two are synonyms, the un- is literally superfluous. There is, however, a distinct use for "unthaw" as a verb meaning to thaw something after it had been frozen (sometimes metaphorical). The word "thaw" can be a verb or a noun.
Seasonal changes (e.g. the spring thaw) are clearly melting or unfreezing already.

Answer 2

Through ignorance. To thaw means to unfreeze. People recognized it as something being negated, but they didn't really have a grasp of the meaning of the word "thaw", hence combined the negation prefix with the word they didn't really understand, but knew it had something to do with the process and voila! "unthaw" was born. Ignorance is and always has been one of the most vigorous agents for language change, as this example shows. People are quite capable of saying things out of ignorance which mean the exact opposite of what they intend. Another good example is when people say "I could care less" when what they mean is the exact opposite: "I couldn't care less." (In other words they care about it as little as it is possible to care, which means not at all.)