Due to postprocessing intentions of my document I need to include comments in the PDF-filer that I generate. Using pdfsquarecomment, everythings works fine. I need to use pdfmarkupcomment though - and this is where I do have problems.
Creating simple minimal working examples, I can perfectly highlight anything I want. Even using more sophisticated testcases, the highlighting works fine. Once I use some external .tex-files (located in subdirectories) that I do include in my document, the pdfmarkupcomment-commands are ignored completely (pdfsquarecomments work all right). I do not get any errors, the PDF gets generated all right - but simply without the comments.
I am using texlive and the LaTeXpdf converter.