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.
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