I'm not really following your problem, but here are some ideas that may be of use to you.

Since you are parsing strings with multiple newline characters, perhaps the /m modifier would be of use. Search for //m in perlretut.

You may have special characters in your regex, so you may need to use the \Q..\E escape sequences.

Perhaps the CPAN module, Hardware::Vhdl::Lexer, does something similar to what you are looking for. I have not used it, but poking through the source code may give you clues if/how the author parses VHDL comments.