Help, Switch over from RB1100AHx2 to RB1100AHx4 not working

Help Please, I am Switching over from RB1100AHx2 to RB1100AHx4 and have copied all my scripts across, modified the layer-7 protocols etc. added extra for bit-torrent blocking ( tested on AHx2 ) everything seems OK, so I swapped them over and nothing is working, nothing, except I can log on to it. I must have done something wrong but what?, everything looks the same except for the slight mods.

My AHx2 is on 6.3.1 and the AHx4 is on 6.42.7, I use the switches without a bridge on the AHx2 and a jumper cable between ports 5 and 6, it is flat out every day and I am changing it over because I have had an upgrade to my fibre cable and need a higher port speed.

The problem is JUMP form 6.3.1 to 6.42.7

There is FORMIDABLE change in the ROS http://forum.mikrotik.com/t/v6-41-current/114978/1

Try to downgrade to 6.40.9 bugfix which is the last version which is compatibile with 6.3.x line