Why are the mark and space tones of these FSK signals reversed? I'm working on a project involving FSK-modulated signals. I'm trying to reverse-engineer these signals to determine the preamble pattern used, because the protocol is proprietary. 

Shown below is a plot of the real parts of two captured transmissions that seem to follow the same pattern - except their frequencies appear to be inverted. This is further evidenced by the instantaneous frequency plots also shown. I captured these signals using an RTL-SDR dongle, which outputs complex I/Q samples. What does this mean?
The apparent exchange of preamble symbols between mark and space in separate transmissions indicates that the packet is differentially encoded in some way.  NRZI encoding is used in both Packet Radio and AIS, so you might wish to investigate if that appears to be the case for your unknown packet format as well.