This article is from the PGP FAQ, by Jeff Licquia email@example.com with numerous contributions by others.
Version 2.3a introduced the "pkcs_compat" option, allowing the format
of signatures to change slightly to make them more compatible with
industry standards. (See question 2.1.) MIT PGP, because it uses the
RSAREF library, is unable to understand the old signature format, so
it therefore ignores the signature and warns you that it is doing so.
This problem comes up mostly with old key signatures. If your key
contains such old signatures, try to get those people who signed your
key to resign it.
If an old signature is still vitally important to check, get a non-MIT
version of PGP to check it with, such as ViaCrypt's.