Hi,
I finally found the problem. The problem in this case was a hardware one. Being a custom board the PCB layout for the second camera had longer links. After some checking realised that the 56mhz pixel clock signal was not going to the imx6 cleanly so when putting the scope probe to look at the signal the out of sync capture became good. Soldering a small 20pf cap across the pin an the ground near the imx6 fixed the issue.
This is quite good result for me.
There is good advantage from my design as it uses both imx6 ipu's which are not used in the reference SabreSD board which uses one ipu to run two cameras. For me this helps as the IPU_prt_enc driver can be duplicated without BSP code change and can support two cameras concurrently. When one IPU is used this can be achieved with the official BSP only by using IPU_CSI_enc for the second driver. However this driver has less features then IPU_prp_enc driver.
Makis