Describing this as a limit on "CS programs" is a common, but erroneous, understanding of the proposal limit.
This specific solicitation — CISE Core Programs — has a 2-proposal-per-year limit. However, that only applies to this solicitation, and only counts proposals submitted to this solicitation. CISE Core Programs is an important CS funding mechanism, but there are quite a few other funding vehicles within CISE (Robust Intelligence, RETTL, SATC, and many more, including CAREER). Each has its own limits, that generally don't count or count against the Core Programs limit.
This specific solicitation — CISE Core Programs — has a 2-proposal-per-year limit. However, that only applies to this solicitation, and only counts proposals submitted to this solicitation. CISE Core Programs is an important CS funding mechanism, but there are quite a few other funding vehicles within CISE (Robust Intelligence, RETTL, SATC, and many more, including CAREER). Each has its own limits, that generally don't count or count against the Core Programs limit.