Boiler prob water not circulating despite new pump and flush

My boiler is driving me crazy!. It (Potterton Profile) just does not stay on long enough to heat anything. I have drained the system, flushed it, replaced the pump and still no luck. It seems as though the water in the boiler is heating up, but not circulating, which means the overheat thermostat cuts in and trips.
It is fully puimped, but not sealed, with the pump pumping downwards. It is all on the first floor and the header tank is only about 2ft above the boiler. There is also a strnge looking fitting at the top of the fill - return loop, which I take to be some sort of air seperator (though as it appears to be sealed and has no valve on it I am not sure how it works) Could this be faulty/blocked? It seems that the water pipe gets hot up to this point fairly easily, but then seems to take ages to warm up on the down side of it (where the pump is connected).
Any clues on how to fix this would be gratefully received. Thanks, Mike

There's air in it somewhere assuming you have opened the pump valves after replacing it. If it's an old system the feed pipe might be blocked which means you have little water in the system.

Let's have some more information, there's not a lot to go on.

It does seem like air (and there is a gurgling noise when pump in switched off), but pump valves are open, boiler and the system have been drained and flushed and feed tank fills the system fine. The base of the header tank is only about 6ins above the top of the circulating loop, the pump is mounted vertically, pumping downwards on the flow side of the boiler and as I men tioned there is a strange looking copper thing (separator I think) at the top of that loop which has the feed and vent pipe connected to it. Plse let me know if there's anything else should i be telling you