tech_support  | 

It's hard to say just how much it's costing you, Bob. Probably not much. Some heat rise in the barrel of the separator could mean your boiler return temperature would be a little warmer than it should be, resulting in lower delta T and lower efficiency. However, that's assuming the same flow rate in your primary and secondary, which is not common. If your secondary flow is greater than your primary flow, you'll have downward flow in the barrel of the separator and your boiler return temperature will be the same as your secondary return temperature. So that is OK.
Perhaps the more important issue with your configuration is reduced air separation effectiveness at the automatic vent at the top of the separator. Hot water more readily gives up entrained air than cold water does, so it will take longer to remove air from the system the way you have it piped.
Take a look at Caleffi idronics issue 15 for more information on separation principles.