Wow, go me! I managed to dork up my site for awhile. :-/ Well I updated my Gmail greasemonky script to work properly even when changing between multiple Gmail accounts. Gmail changed something awhile ago, and I was slow to update the version on the site. It’s there now.
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: 
As everybody and their mom has been talking about Greasemonkey and AJAX, I decided I had better get a piece of the action. I also had a growing annoyance with the state of MUAs. I was contemplating writing my own, however I’ve since realized that perhaps I can get what I want by using Greasemonkey to add features to Gmail. Persistent Persistent Searches is that first step. The bit of code that I wrote allows people to write Greasemonkey scripts that store data in a Gmail contact. I wanted it to be relatively secure, “nice” to Gmail’s servers, and easy to use. What I ended up with is something that stores data in the note field of a particular contact. The data resembles cookie data and can be used in a very similar fashion. In fact the note data is cached in a cookie. This is my attempt to be nice to Gmail’s servers. On initial login, the note data is downloaded from the contact and stored in a cookie. Any read attempts for note data actually just read the local cookie. Any write attempts change the data in the local cookie and on Gmail’s servers. Since this data is cached in a cookie, I was a little concerned with the expiration time of this cookie (so that other users on the same computer couldn’t see the cookie data). The pseudo-solution was that this cache cookie expires after 3 minutes. However, Gmail checks for new mail every 2 minutes. Each time this happens (and the same user is logged in), the cache cookie will be given another 3 minutes to live. In other words, this cache cookie will be around after the user logs out of Gmail for at most 3 minutes.