When Jhove finds a parenthesis inside a string in a pdf file, it says that the file is not well-formed, while the pdf reference allow to include pairs of balanced parenthesis inside strings.
I have attached a tar.gz archive with four files:
test1.pdf with a balanced pair of parenthesis inside a string.
test2.pdf, which is the same but with a pair of square brackets instead of the pair of parenthesis.
jhove-session.txt, which is a recorded session where you see that Jhove (Rel. 1.11, 2013-09-29) says that test1.pdf is not well-formed, and test2.pdf is well-formed and valid, while both are well-formed and valid.
README with some more details provided, so anyone can reproduce the session.