I compiled and installed hunspell 1.2.12 under cygwin (latest version, latest compiler tool chain) and installed latest open office dictionaries.
Now, when checking a latex document using en_US dictionary, hunspell complains about negative numbers being misspelled, no matter if the number occurres in regular text or in equation environments.
Maybe your dictionary uses more strict rules for checking words with hyphens. In this case, removing the BREAK lines from the .aff dictionary file could help.