So I'm just starting to build my pedalboard and atm Ive only got two pedals, a Boss ML-2 for distortion and a NS-2 for the noise reduction.

Its set up like this: guitar -> NS-2 input -> send to ML-2 input -> return to NS-2 -> amp (clean channel), which I think is the right way to do it.

The only problem is that when i play something, the volume gradually increases over about one second, as if it takes the Noisegate 1 second to realise something is playing and to let the sound through, but once this happens it sounds perfectly fine, until you pause in the middle of a song and start playing again. It makes no difference whether the threshold and decay knobs are at minimum or maximum it still happens.

Anyone know how to fix it? Thanks in advance.
Try running the ML-2 before the NS-2 and without the x pattern. Just straight through from the guitar to the input and output of each pedal int the amp.
Cheers mate, tried that but it squealed with feedback. Put the NS-2 in front and it works perfect.