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It's a bit hard to explain, so I've attached some screenshots.
Occasionally the updater prompts me to update these apps when they don't need to, displaying errors.
Sorry if this is a known issue and threads already exist.
This happens if you somehow manage to launch two instances of the updater. This can only be accomplished when Windows is not working properly and the app is prevented from setting a mutex to ensure it's not started a second time. Some badly written antivirus and antimalware tools can cause this. As can Pokki.
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Hmm okay, although the only antivirus I use is windows defender.
are you using any kind of custom windows start menu or launcher?
Yes, 'Classic Start Menu 3.6.5' because the metro launcher on windows 8 is horrid.
We've found that the Pokki Start Menu screws up a few different bits within Windows. Preventing apps from being able to properly setup a mutex to detect when you launch a second copy, for instance. I'd wager Classic Start Menu has the same bug. You could try disabling it. Or launching the PA.c Platform directly within Explorer. Not sure if that would work around the bug.
I have gotten this error if I manually kick off a check for updates right after the menu starts. I haven't broken myself of the habit so I occasionally still do it even knowing the menu automatically does it on startup. I don't use any custom start menu and use Microsoft security essentials for anti-virus.
Once you go portable...
It's fine to do that. And you'll get a message saying the updater is already running.
If, on the other hand, you get the error seen above in the updater, that means your system has a major issue preventing mutexes and environment variables from working properly. So far, the only thing I've seen that causes this is Pokki and Classic Start Menu. Likely because they are not explorer.exe-based so they are splitting the running apps out into multiple branches of environment variables which messes with app's abilities to talk to each other.
Here is the behavior I'm seeing. http://i.imgur.com/lLOcs2s.png
Is it expected that I would see both the message box and the instance of the updater?
I"m not ruling out that you think it's a system issue but I'm more inclined to think this is a timing issue but I haven't looked at the code to determine.
The timing doesn't matter at all. The updater sets a system-wide mutex as soon as it starts so that it knows not to start again. The only thing it does before setting it is load the translation files so it can show the already-running message in the right language which takes milliseconds (unless something is absolutely killing drive access speed and causing a few simple INI reads to take a long time). The only way it can start again is if that mutex isn't set properly.