What oil was used to fill the system? If the oil was not a hydraulic oil with foam suppressant, it may be generating it's own air from pumping. Drawing a vacuum on the system (and oil) should cause the air to explode out of the liquid, but the next day it may just churn up more air again.
I used to get Barnes and Fenner hydraulic power units that would do that and changing to a better (more appropriate) hydraulic oil solved it almost every time. If you can get your hands on some paraffin oil as an additive it might help.