You need to sort the automation IDs of the Reaktor instrument.
Open the property panel of the instrument and have a look at the bottom of the property dialog.
As you can see the ‘MAX ID in use’ is greater than the ‘MAX ID’ used for automation. Choose ‘Sort and Compress IDs’ form the IDS menu.
After that the IDs will be sorted and compressed.
Now change the MAX ID to the value showed in MAX ID in use.
Save the ensemble. Start recording in Podium and a knob move in the Reaktor instrument should create a automation track now.
Another way would be using MIDI CC messages. But this does not work in Podium right now. For this you need to activate ‘Panel to MIDI’ for the controls you want to automate.