I would recommend that you first confirm that the PCR M50 is working as a MIDI controller independent of Kyma. One way to do this is to connect its USB to your Mac, then use a free utility application, MIDI Monitor, that you can download from here: http://www.snoize.com/MIDIMonitor/. This tool lets you see MIDI messages coming from any MIDI port that OSX "sees". If your PCR M50 is working properly then you should see MIDI Note on and note off events when you press its keys. Since the PCR M50 has multiple MIDI ports defined you will have to monitor all of those to check that there is proper MIDI activity.
If you do not see any MIDI activity then that would suggest that something is wrong with the PCR M50.
If the PCR M50 appears to be working properly in this test then I would suggest that the next step is to check if it is working in KymaConnect. For KymaConnect to work with any MIDI port that port must be assigned to one of its four available EXT MIDI "slots". This is done from the KymaConnect preference pane. In this case you want to assign the PCR MIDI port that carries MIDI performance information, like note events. Comments in your question suggest that this is its second port but you can confirm this in the PCR M50's user guide, or my the results of your MIDI monitor test.
Once it is properly configured in KymaConnect, and KymaConnect is running, there are green status "LEDs" next to each enabled EXT MIDI port. Find the one assigned to the PCR and watch it while you play keys. The "LED" will briefly show a brighter shade of green when there is MIDI activity.
If this appears to be working properly then the next step is to verify that the MIDI information is being received by Kyma. One way to do this is to select the "Configure MIDI" option on Kyma's DSP menu. Once that popup is showing press the "Show MIDI Messages" button to see a display of the latest received MIDI activity.