Tb6600 upgrade to DM542T motors now run badly/noisy!

So I changed my CNC controller from NEVM V1 to V2. This gave me issues with the TB6600 drivers dropping out. After some research I decide to go for the DM542T driver. I thought this would be a straight swap.
My X axis ran better than before. But the Y axis and slave A axis are noisy while in stall position and are not running particularly parallel to each other as if one is running with a delay. The Z axis is a mess. It’s jumpy and doesn’t run well at all. I’ve messed with stepping and motor amps on the drivers and tried motor tuning.
Nothing seems to work. I’m also getting a flashing green power led which I can not find any reference to on the net. Any help please?

Have you read this... http://www.mycncuk.com/threads/11083...ible-solutions

Just a thought.