Thank you, thank you, thank you everyone - what great feedback!

After having a think and reviewing everyone's replies I think it's definitely shoe related. They were okay to begin, but I've had them for 2 years and they've taken some bashings - enduro events and the like. The sole would have definitely softened from their initial levels. I got carbon soled road shoes for my road bike a while back and this solved numbness probs I had with some plastic (yuck) soled road shoes.

I am going to look into some more race/competition based MTB shoes and look to upgrade - I've been trying to avoid this given finance restrictions but it is time

You guys also hit the nail with technique - I tend to do a lot of pushing with very strong quads and not necessary pull up when I should. This would definitely be a factor.

Thankfully hasn't progressed to a Morton's Foot related neuroma or nerve pain as there is no discomfort under the ball of the foot.

One other thing How do I work out correct fit for bike shoes - I'm an ex-runner and have running shoes down to a fine art, but cycling shoes elude me. I have some great LBS's but they also seem to struggle with the details ("do they feel comfortable?" etc).

Thanks again