It sounds like you might have assigned the expression pedal to the other knobs without realizing it.
De-assigning knobs is done the same way as assigning them. If you move the expression pedal, the effect light starts blinkingto tell you that you can assign knobs to the expression pedal. Move the expression pedal to the Heel position and move a knob to the value you'd like it at the Heel position. Next move the expression pedal to Toe and move any knobs to where you'd want them at the toe position. To deassign a knob simply move it to the same value for both Heel and Toe. After you have made expression pedal assignments you must save your Preset. Press and hold the Encoder knob for a few seconds and select the Preset slot you want to save to. Then Press and Hold the Encoder Button again to save.
Whether you are in Play Mode or Bank Mode, saving a Preset is done the same way. The saved Preset can be used in either mode.
As far as unlocking extra Presets, the newest software update for TimeFactor doubles the amount of space for storing presets.
To check to see if your TimeFactor's Software needs to be updated, read this:
TimeFactor Software Updates can be done from this page: