For noncommercial use, use the MIT version. There are no RSA patent licensing problems with that version at all. It is fully licensed. Some people complained that the older versions of PGP could not read the stuff produced by the new legal versions. Look, when you have a new version of a spreadsheet come out, it can read the old files, but the old version can't usually read the new files.
Nobody complains about that.
This is the same thing. A version byte changed, which says what version of PGP is being used. No algorithm changed. The old version can only read messages encrypted the old way, and the new version reads both. The reason for it was to make peace with Bidzos, but some people on the Net didn't like that.