You did not say WHICH HP 1090 Pumping system you have. There are several different versions (i.e. PV5, DR5, TR5). Does the problem occur on all pumping channels or just one (A,B,C) ? The High Pressure booster pumps are very reliable and when they do have issues they are usually related to one of the following: Inlet and Outlet Valve Cartridges and frit or Diaphragm. Sounds like you may have addressed these. However, did you service the low pressure syringe pump(s) for the channels ? What about the rotary valves on the syringe pump(s) ? These are responsible for most of the problems related to maintaining flow and pressure. The rotary valves are famous for leaking internally and each one can cause all kinds of problems all by itself if not properly maintained and serviced. I have seen many inexperienced cleints and experienced service engineers ignore these parts when servicing the 1090. Many do not even know how the systems work and often think that the high pressure pump alone drives the solvent flow. It does not, as it works in tandem with the low pressure syringe pump(s). Everything must work perfectly. Each syringe pump should be regularily stripped down, cleaned, inspected and parts replaced as needed. The syringe pump(s) are located directly behind the solvent cabinet (two pozidrive screws to remove the cabinet).
Lastly, I will assume you are running the system with ChemStation software (maybe you are not ?). ChemStation has a nice diagnostic feature to view the raw data that comes from the Low pressure and high pressure flow side (LP1, LP2, HP1). Bring up the diagnostic window to view the data as it can be useful in diagnosing the problem (diagmon).
Sorry, we are not in the UK so can not suggest a qualified engineer.