Neville one question, what processor are you running?
The basic machine sounds okay but I reckon most of the trouble will be with your graphics card, you'll probably want to change it for a GeForce Ti card

Yup it is the graphics card that is the problem then!
I'm running a PIII 1Ghz with 512mb RAM and a Ti4600 and getting pretty good results.
Look around at Ti cards, a 4000 series will do, but a 5000 series kicks bottom

I recommend you have a good luck at the 6600GT 128MB AGP version.  They are not expensive and offer such a performance increase over the 440.

You will go from  to  with one of those.

Thanks to all, Your help is much appreciated, with all the inputs have managed to solve majority of the problems. The joystick conflict was because of another USB joystick which was plugged in for remote control flight simulation so the Brakes and the rudder conflict is solved most of the graphic issues have also been solved.
The only issue which remains is the water, which looks very artificial and of a unnatural blue color.
Could it be some graphics setting in Windows as I have just reloaded XP and service pack 2??

Get a 6600gt. The 6600 vanilla is a poor performer for its price.

BTW, when installing the new card, did you reinstall the drivers and delete fs9.cfg?

Cause that may be the problem.

I couldn't find the cfg file I was thinking of in FS9, it must have been an FS8 issue, sorry.

Make sure you don't mistake the 6600GT for the 6600, the 6600 often comes with lots of slow ram and  is not near as good as the GT model, which is commonly made with 128mb of quality, high performance ram.

Look for Lemoncat's water texture replacements in the FS9 scenery downloads, or ask in the forums where to get them. Lemoncat is often in the screenshot forum.

Turning the water effects and reflections off will give you much better performance on your MX440 and it will render the water much darker as well. Clouds will kill your  framerates, so turn them off when you need performance, ie. landing in busy airports with lots of scenery.

Unfortunately, FS9 doesn't render well on older equipment, I had an overclocked MX460 and it was disappointing. I went to a TI4200 128mb 8x AGP card, a bit better, then a FX5900XT O/clocked to an ultra, still lacking, now I have a 6600GT and it's finally reasonable.
So, you can waste lots of time and money like I did, or just get something decent to start with.   8)

There are basically 3 slot types of video cards currently on the market, PCI, AGP and PCIexpress from oldest to newest. There is also "onboard" graphics on many mainboards.
AGP comes in a few flavours with 4x and 8x being common, PCI cards are generally used to try replace onboard graphics where a board doesnt have an AGP slot, (a dubious solution), and PCIexpress offers the newest and fastest interface.

If you buy an expensive video card, you need to consider that an AGP type may be incompatible with any future mainboard upgrade you wish to buy. So, if you plan on buying a new system in the near future, best to wait and get a PCIe video card on the new system.

It's in your interest to post your system specs here so we can suggest the best upgrade route, for without your detailed specs, we can't offer any solutions tailored to you.

An accurate mainboard ID number with revision number is adequate, Look at your mainboard itself and read the actual ID there. It will say something like "MSI 845 Pro2-R" or something equally unintelligible.... the revision no. is sometimes near a corner of the board, sometimes near the name. Also, if the PC is a Dell, Compaq, HP etc., please warn me off in advance.