Thanks for your bug report. This one is a little bit tricky because of the way it has evolved over time.
If you are connected to a server:
/ignore nick
-> adds item as network specific.
/ignore -w nick
-> adds item as non-network specific.
These are considered different items.
If you are NOT connected to a server, a network name is not available, so:
/ignore nick
-> adds item as non-network specific.
/ignore -w nick
-> adds item as non-network specific.
These are the same item.
One potential issue is that when /ignore updates an existing item, it moves it to the bottom of the ignore list. The same applies if you edit an item in the control dialog; it gets moved to the bottom of the list. I will see if I can change this behaviour so that the item stays in the same place when updated.
Other than that, the behaviour appears to be correct.