Just wanted to share the solution found as it took me ages as mcc does not provide any reference to which files cause the warning messages ...
(BTW - mcc on Windows runs just fine without these warnings.)
The cause is the presence of non UTF8 characters in m-code. MATLAB on Linux has UTF8 as default character set whilst MATLAB on Windows may have a different character set such as windows-1252.
Use
feature('DefaultCharacterSet')
to determine this.
Anyways - it can be a pain to identify the m-files that cause the warning. The linux shell command below helped me a lot:
find . -name *.m -type f | xargs -I {} bash -c "iconv -f utf-8 -t utf-16 {} &>/dev/null || echo {}" > utf8_fail
