Google decided to change the domain and URL syntax of Gmail:
My persistent searches script has been updated to work with these changes. I would recommend uninstalling the original script and then installing the updated version.
It appears that the issue is that behind the scenes (or at least relating to search and filters), labels apply to individual messages. Apparently when a filter is set to add a label, it will add that label to the message, and not to the conversation that the message is a part of. This is the only way that different messages in the same conversation may be labeled differently. Every other interface that Gmail provides to the label functionality relates to conversations, not messages. This turns out to be annoying. :-/
I’m using Gmail a lot more recently (more later), however I’ve found an annoying bug. I’m now forwarding all my messages to a non-Gmail account to Gmail. All of these are given a label to indicate that they came to that non-Gmail account. They are also optionally given additional labels depending on if they have certain subjects, recipients, or content. I want to be able to do a search for any messages that only have the initial label that indicates that this email came through my non-Gmail account. For instance, if I label all my bills as “bills” and all emails from my gas company as “gascompany”, then some emails may be labeled both “bills” and “gascompany”. However, when I do a search like [label:bills -label:gascompany], I sometimes will get messages that are labeled both “bills” and “gascompany”. For those that are showing up in my results (but shouldn’t be), I can manually give them the “gascompany” label (again) and they won’t show up in the results if I do the same search again. Here’s proof: 