Front mech shifting - not working at both ends of cassette

I presume you've shifted to the inner ring then undone the gear cable completely and lined up the derailleur using the L stop screw so that in 39/25 the chain barely misses the inner cage plate and then re-attached the gear cable?
This should then set you up so that the shift to the big ring works without shipping the chain.
If it still does then your chainset might well be sitting too far out along the axle OR the bottom bracket is too long?
One thing I couldn't understand though is why would you want to change from 53/12 to 39/12 anyway? It seems a very strange gear ratio change that wouldn't normally be used except by newbie's? (no disrespect intended)
Cross chaining isn't ideal anyway and puts sideways forces on your chain that you don't want both in terms of wear & efficiency.
What shifters are you using out of interest?

Cheers - got it sorted now, and yes was starting with inner plate just missing the chain. I think my desire to get those ratios working is because it's a bit annoying to have to think "don't shift up to big ring" when you're in 39/12 - then have to move back down the cassette before being able to move up the front chainring! Also, given the price you pay for a modern groupset, I would like to be able to shift it around any way I link (and I presume they are engineered to withstand the tollerences set by their own kit)...

@ Señor Bear - there're not many ways to take pictures of the bottom of your bike and easily shift between the gears when you don't have a workstand, but appreciate the pictures aren't massively intuitive