All characters of string 2 are in Latin1, but some characters in string 1 are beyond codepoint 0xff.

I'm making a guess: your program handles decoding not properly, and so you end up with string 2 encoded as Latin1 and string 1 decoded into Perl's internal format, which – when passed into the world outside the program – accidentally does the correct thing.

This explanation fits the symptoms, but since you did not show any code, we can't be sure.