Hello Hans,
Thank you very much for your message. The PIO program reported 'PE6<0><0><1><1>' for both U-Boots but changing the configuration's CONFIG_AXP_ALDO3_VOLT and CONFIG_AXP_ALDO4_VOLT back to 2800 did indeed solve the problem. I can run U-Boot 2016.01 now and control PE6 properly.
LDO3 is connected to pin F19 in the Olimex schematics (VCC_CSI0, in the A20 datasheet mentioned as Port E Power Supply) and LDO4 is connected to pin E18 (VCC_CSI1 mentioned as Port G Power Supply).
So would the change in u-boot make sense by setting the default to 0 now? I'm not sure if the git remark 'LDO3 and LDO4 are normally either unused, or used to power csi attached camera sensors' is correct as it seems (also?) to be the source or reference for the A20 chip pins itself..? At least this is the case for multiple (all?) Olimex A10/A20 boards (I checked A20-SOM, A20-LIME2, A20-Lime and A10-Lime).
Regards, Hendrik