Okay tested it and I know which line causes the problem it's
data.raw["roboport"]["basic-roboport"].energy_usage = "10kW"
Whenever I change it back to 0 remove the power from all the roboports and then hook them back up they work perfectly. I also tested this with construction robots first placing a roboport and then placing a pylon also then it works.
For some reason you want the roboport to use power while it's idle I don't know why but this seems to screw with the system thinking there is no power.
The line should be as follows
data.raw["roboport"]["basic-roboport"].energy_usage = "0kW"
I also want to have a flow_limit of 5 but for you i have the lines here.
This has to be copied in data-final-fixes.lua if you hadn't figured it yet.
Copy these over your's and it should be fixed.
data.raw["roboport"]["basic-roboport"].energy_source.buffer_capacity = "1MJ"
data.raw["roboport"]["basic-roboport"].energy_source.input_flow_limit = 0.5 * settings.startup["roboport-charging-rate-multiplier"].value .. "MW"
data.raw["roboport"]["basic-roboport"].charging_energy = 1 * settings.startup["roboport-charging-rate-multiplier"].value .. "MW"
data.raw["roboport"]["basic-roboport"].energy_usage = "0kW"
data.raw["roboport"]["basic-roboport"].logistics_radius = data.raw["roboport"]["basic-roboport"].logistics_radius * settings.startup["roboport-logistics-radius-multiplier"].value
data.raw["roboport"]["basic-roboport"].construction_radius = data.raw["roboport"]["basic-roboport"].construction_radius * settings.startup["roboport-construction-radius-multiplier"].value
data.raw["roboport"]["roboport"].energy_source.buffer_capacity = "1MJ"
data.raw["roboport"]["roboport"].energy_source.input_flow_limit = 0.5 * settings.startup["roboport-charging-rate-multiplier"].value .. "MW"
data.raw["roboport"]["roboport"].charging_energy = 1 * settings.startup["roboport-charging-rate-multiplier"].value .. "MW"
data.raw["roboport"]["roboport"].energy_usage = "0kW"
data.raw["roboport"]["roboport"].logistics_radius = data.raw["roboport"]["roboport"].logistics_radius * settings.startup["roboport-logistics-radius-multiplier"].value
data.raw["roboport"]["roboport"].construction_radius = data.raw["roboport"]["roboport"].construction_radius * settings.startup["roboport-construction-radius-multiplier"].value