Compatibility with proprietary dependencies that the company cannot control. If I'm not mistaken, GPL requires the release of the dependencies' source code too if there are no other implementations around.
I would be happy to hear from anyone who knows about this subject if what I'm saying is correct.
It depended on whether the programs were distributed together. So it wasn't okay to link against OpenSSL for GNU/Linux distributions (although interpretations varied). For a time, this was used to push GNUTLS as an alternative to OpenSSL. But it was generally agreed upon that it was okay to link against CryptoAPI on Windows because you would not distribute Windows code along with your GPL binaries.
I would be happy to hear from anyone who knows about this subject if what I'm saying is correct.