Nets are not connected correctly into hierarchical in PADS-PCB netlist output. This problem may occur with other outputs as well. I have not checked them.
When creating a hierarchical symbol, pin numbering cannot be set by the user. Instead, it starts at 1 each time the pin button is clicked. This can often result in duplicate pin numberings. This affects netlist output.
In PADS-PCB netlist output, nets are connected into hierarchical elements by having the hierarchical symbol pin as a common pin among nets. Since the hierarchical symbol pins can have duplicate numbering, this results in merged nets.
On a related note, I don't know that the layout software that reads the netlist will even interpret the net connections correctly, since the hierarchical elements are not components. It doesn't know, for example, what "H1.1" is since H1 is not in the part list.
Update:
I looked into the netlist some more. It looks like the netlist is still functional. The proper net connections are made in addition to the hierarchical pins being added as connections.
I haven't verified that all connections are correct in my netlist yet, but it seems that the fix may only be to not add hierarchical symbol pins to the list of pins under a net. For example, if R1 resides in hierarchical element H1, and R1.1 is connected to the "INPUT" pin in the hierarchical symbol, which is GND in the high level schematic, R1_H1.1 should be in the GND net. Right now, H1.x also appears in the GND net, where x is whatever pin number the "INPUT" pin ended up under.
However, if the layout package merges nets that have common pins, then having duplicate hierarchical symbol pin numbers could merge nets where they should not be merged. Ensuring that there are only unique numbers for the pins in a hierarchical net would prevent this possibility.