This is the reset procedure for resetting Climatronic units in a Skoda Fabia Mk2 and Roomster in the later models. If your air-con purges away or goes hi-low when in auto (at a fast rate), then the system may benefit from a recalibration.
1. Ignition to 2nd turn
2. Wait for the unit to start
3. press and hold a/c, face fan, and windscreen clear (max up)
4. Wait for about 45s for the system to run through all settings and return to the previous setting
5. Job done - I hope this solves the issue if you have it.
If this doesn't help, unfortunately it could be the recirc. or air-position flap actuators.