OK, you asked for it...
A Power Commander (PC) is a 'black box' that sits between the cable connections to the fuel injectors (I hope you know what a fuel injector is
) and the injectors themselves.
It intercepts the timing signals from the ECU which tell the injectors when to open and when to close and thereby determine how much fuel is injected into the cylinders and when during the engine cycle. This varies with engine speed, load, engine temperature, ambient temperature, throttle position etc. etc.
The 'black box' has a memory into which is loaded 'standard' maps for various modifications such as silencer, camshaft etc. These Power Commander maps alter the fuelling either up or down by certain amounts in 500 rmp increments.
This Power Commander mapping over-rides the stock ECU mapping and can overcome lots, if not all, of the peculiar fuelling issues on the stock bike set up.
By putting your bike on a dyno (with a dyno operator who knows their arse from their elbow) they can produce a custom map for your bike with your mods and to suit your riding style.
A Power Commander does NOT increase the power of the motor appreciably (perhaps the odd bhp or two) but does iron out all the glitches inherent in any given bike set up.
Someone fitted the Power Commander to your bike in an attempt to 'fix' the extremely bad and erratic fuelling of the stock bike.
However, unless you know what the map is in the PC, you have no idea what your fuelling (timing and fuel volume) is. I would wager my remaining testicle that this is the source of your dreadful fuel economy.
Somewhere on your bike, under the seat, behind the fairing or wherever, is a fag-packet-sized box with 'Power Commander' printed on it. It has a mini USB port into which you can plug your computer. You need to download the Power Commander program and install it on your computer. This will allow you to see what the map is that is installed and whether it is a standard Power Commander supplied map or a Custom map created specifically for your bike by a dyno run, or, heaven forfend, a 'bodged' map created by a previous owner by hitting the '+' or '-' buttons in 500 rpm increments.
Any fool can create and save a map in this way and the results, without a dyno run, are ALWAYS A DISASTER!
Your first step is to find the PC. Start at the throttle position sensor (to which the Power Commander is connected for its power supply) which is on the right side of the bike, behind the fairing and inside the top frame member. With experience you can spot this easily. Without it, you are better off taking off the right side fairing panel and tank panel. Once you find it, you can follow the 'non-standard' cable from there and that will lead you to the Power Commander.
You can contact Power Commander (at Dynojet) on this link...
http://www.powercommander.com/powercommander_ex/... and they are extremely helpful.
So, find the Power Commander, install the Program on your computer and interrogate the module to see which map is installed.
To figure what to do next you will need to know which silencer you have installed. PC have 'stock' maps for all sorts of bikes with any number of silencer combinations. You should 'save' the current map so you can reinstall it if need be.
Then, replace that map with a 'Zero' map. A Zero map means that the Power Commander neither adds nor deducts any value from the ECU mapping and the bike is then running as BMW intended. Having 'saved' the original map, you can re-install it at any time.
All this sounds very techie and complicated but in reality it is all well documented on the Dynojet website and the program is very user-friendly and intuitive.
Having done this, I predict that your fuelling will be less than perfect at low to medium rpm and road speed but your fuel economy should return to the normal high forties range.
From there, the world is your oyster and you can arse around with the fuelling until you are blue in the face and the bike implodes...or you can leave it as is or spend £100 on a dyno run at a place that understands Power Commanders (almost all dyno facilities) and have a custom map produced for you and your bike.
Here endeth the lesson.
PS Don't think about simply 'disconnecting' the Power Commander (the bike will not start or run) or 'removing' it unless you are into open-heart surgery.
If you need more help, just shout.