Do I need the fluid cell cap on during measurements?

Yes, the fluid cell cap or shielding cap also acts a shield against external electronics, which can make the baseline more noisy and hinder your efforts in getting a good measurement. If you are still observing electrical noise or 'pulses' in your trace, move the Exoid away from electrical or transmitting equipment. 

Also ensure you close the lid of the Exoid once your fluid cell (with shielding cap) setup is complete.