OK, since you added more stuff after your edit, here are the answers you were looking for:
So, what exactly is "operating budgetary balance"?
OBB = (Total UK Expenditure - administration cost paid by the UK) - Total UK contribution x (total EU expenditures – Total adminsitration cost) / Sum of all national contributions to the EU budget
And what is causing the disparity between OBB and revenue-expenditure?
Many things, (UK rebate, administration costs etc...)
For 2008, it equals -844, exactly what both websites say. You could have drawn the same conclusion downloading the data and checking the formulas.
And yes, OBB it's a good indication of the net contribution. It's the official indicator of the Net Contribution used by the European commission
The Commission’s list of net contributions is based on a method which uses the individual countries’ contributions in the form of own resources, such as VAT and GNP, as the basis for the calculations
If you wanted more info you could have read the link I provided:
First, the extent of the individual country’s contribution of VAT and GNP as a percentage share of the total contribution of VAT and GNP is calculated. The resulting percentage is used to calculate the amount the Member State should receive from the EU if there were to be a balance between payments and receipts between the Member State and the EU. If, for example, a country’s contribution amounts to 7% of the total contributions, the country should also receive an amount which corresponds to 7% of the EU’s total payments. The net contribution is then calculated by looking at the amount the country actually receives from the EU, from which is deducted the amount the Member State should receive according to the above. Finally, the individual country’s contribution to the financing of the British rebate is also deducted.
As regards this:
an example, OPs source for 2008 of revenue (10.1) - expenditure (7.3) = 2.8 billion. In my mind that means that the UK contributed 2.8 billion to the EU that year, but your link goes off "operating budgetary balance" which has 2008 as a net contribution of 0.8 billion from the UK.
No that would be the exact opposite.