I have just changed the filter and cover plate on a 2005 RRS and have refilled the fluid I have only managed to get about 5.5 litres in the box, is this normal? I have done everything as per the book i.e. Filled it with 3-4 litres and then started the car and ran it through the gears and then topped it up but only got 5.5 litres in...

Did you top it up with the engine running? Otherwise you can't get enough in there. How much did you drain out? Doing it the way you have, it's recommended that you do a double flush, so change it again in a few miles.  Bodsys Brake Bible
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Did you use the correct sump and filter, or the BMW tin thing, there is near enough a litre (2 pints for old timers) more oil in the correct sump.
I am not able to get a double flush in Spain, however I just had my oil and filter changed, and will change the oil again in a week or so, and yes my car had the genuine sump fitted.

Only circa 40K on my car, however there was a little crap on the magnets. In Spain - 2018 F Pace - Frightened away from the Sports due to crank failures
Gone - A couple of RRS, A couple of Disco's. However thinking of another Sport.

5.5 litres is around what comes out with a sump change.

Gearbox has a capacity of 11 litres

I did top up with the engine running bodsy.
I bought the full kit from Maltings off road with the oil supplied (D3-MV Rock oil) new filter and metal sump cover SRE
I presume that the remainder is in the oil cooler and pipe etc. Disco_Mikey

Worst happened today when I was driving the car it started to judder and felt like clutch slip...when I got home I checked the oil and it looked a reddy brown colour so I drained it and replaced it...I will see what tomorrow brings.

Torque converter, valve body, cooler and pipes etc.

The torque converter holds around 4 litres on its own

My Car cost me a lot of my hard earned as my Sport is a Spanish car, it cost me a LOT more than a UK car so I do not see the point if penny pinching when it comes down to a simple thing like oil and filters. To my mind, fitting the correct parts let alone "mixing" different oils is cheaper than a new box.
Still at the end of the day, is down to the individuals choice, you pay your money, you take your chance. In Spain - 2018 F Pace - Frightened away from the Sports due to crank failures
Gone - A couple of RRS, A couple of Disco's. However thinking of another Sport.

SRE I was told by I was buying the best replacement kit best filter very best oil and I did research what the best options and this did seem the best...
I will be speaking to the supplier in the morning!

It is recommended to reset the adaptations of the transmission ECU after a gearbox oil change. You'll need a suitable diagnostics tool to carry out the reset routine so maybe a trip to a specialist is in order? Bear in mind that it is normal for the gearbox to behave a little oddly for a while after a reset until it adapts itself. Don't know if this would help your issue but worth a try? 2008 MY Java Black TDV8 HSE