I can't offer any explanations why it isn't working for \n\r but I can offer some suggestions:

undef $/;
$filecontemts=<DEFILE>
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will slurp all of the file into $filecontents, then you don't need to worry about using join.

print "Changing \"$File::Find::name\" file...\n" if ($happens=($file_c
+ontents =~ s/$changefrom/$changeto/g));
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should make the substitution and return the number of times it happened all at once. It will only print if $happens isn't zero. It's a little hard to read, but you get used to it quickly. Then you are only doing one regex on the data, rather than two. (vice versa for case insensitive matching.)

I don't know if if($code =~ m/yY/) would be faster than testing for equality, but it is easier to read (at least for me anyway. YMMV)