SNR

Wiring set up as follows:
BT Master socket - DSL Filter - Netgear DG834 (No extension)
BT Master Socket (Same as above) - DSL Filter (Same as above) - House phone on an extension from filter.
My question is would this extension cause my noise margin to fall. I have unplugged the phone and the margin rose by 1db? Is it better to plug the phone directly into the filter?

A 1 dB change is not really conclusive.
"Is it better to plug the phone directly into the filter?" Why not try and see, you might get that 1dB back. Personally I dont think you have anything to gain.

The wiring's fine. It's better to have a central filter as you've set up as this will help reduce any pickup on the extension cable itself interfering with the broadband. 1dB really isn't a significant difference, and in fact it may just be inaccuracies in the modem stats responding to line impedance changes rather than an actual SNR change. However if you want to experiment then you could look at improving your filter, or alternatively putting in a second filter on the phone extension.

In reply to:

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alternatively putting in a second filter on the phone extension.

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Sometimes two filters together interact, so trying different types may be necessary. A Voyager 105 USB modem with the frequency / SNR graphs is a handy tool for this sort of thing, see what happens when the phone is plugged in, taken off the hook etc.

Moved the main phone so that it is plug directly into the filter even changed the filter my margin has gone to 6db but my upstream margin has gone from 22db to 18db. My connection speed is 4384 but my profile is currantly set low because of a disconnection yesterday, am I right in thinking that this sort of thing takes at least 3 days to recover from?

Yes, about 3 days.