I have been struggling recently with a custom ground symbol in my scematic. Everything looks Ok in eeSchema, but when designing the board layout It showed no connection between these ground symbols. Pretty annoying, because my board would not work that way.
I checked the ground symbol, and it was defined as ‘power port’ and it has a pin named “GND” so all looks OK?
I took some time to discover that the symbol only connects automatically if you set the pin ‘Invisible’ (in the library editor under “Pin properties”). My pin was ‘visible’ and thus no automatic connection. Setting the pin as “invisible” and “Power input” solved this problem.
The pin name remains visible in the schematics by the way, unless you switch the pin visibility off in “device properties” or on your schematic.