Many of the non-compatible programs have programming flaws dealing with null pointers and handles. Because the Macintosh OS uses only 24 of the 32 bit address lines, many programmers have taken short cuts to handle locking by using one of the eight non-utilized bits as a locking status bit. But A/UX recognizes all 32 bits, and programs using those upper eight bits as status have major problems.
A/UX 2.0, 2.0.1, and 3.0 have a 24-bit compatibility mode (it is a login session type) that will allow customers to run older, poorly behaved applications.