If you are using a monotimbral synth, then you can use the same mapping for both MIDI and audio routing, and Podium will then automatically compensate for latencies in the audio and MIDI interfaces. Take a look at the ‘Yamaha AN1x’ library file to see how a monotimbral synth can be configured with a single mapping.
If you use multitimbral synths, then you need to work with separate mappings for audio and MIDI channels and thus the association between audio and MIDI is broken, and latency compensation is not performed. I’ve been thinking about this. What I need to do is implement a global instance number for the hardware mappings, similar to the instance number used in multitimbral plugin mappings. This instance number is what enables Podium to link together different mappings for the same device and perform proper latency compensation. I’ll add it to the future list.
If this does not explain your problem, then mail me the project file so I can verify your setup.