Complex sentence: SFU 1.0 and 2.0 used the MKS Toolkit; starting with SFU 3.0 (1999), SFU used the Interix subsystem.
Split into simpler sentences: SFU 1.0 and 2.0 used the MKS Toolkit. Starting with SFU 3.0 (1999), it used the Interix subsystem.