Not sure if these are actual issues -
I had the AquaSnap beta installed, and am using the launcher beta 5. I ran the 'update apps', and it's trying to d/l the AquaSnap but gets a '404'.
Also, I have the Java Portable installed, but it haven't spotted the jPortable update. As its not visible in the menu, I'm rather unsure which version I have installed at present.
Java Portable isn't an app, it is considered an add-on, and (at least for now) is outside the scope of the updater. You will have to update it manually.
To check what version you currently have, browse to /PortableApps/CommonFiles/Java on your portable device and open JavaPortable.ini. This file will tell you your current version. (eg. 1.6.0_22 means you have Java Portable 6 Update 22)
I know the issue at this time till John can fix the issue would suggest getting it from the home page., as Aquasnap is freeware it can not actually be posted on Sourceforge which is where the updater appears to be looking for it
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Fixed AquaSnap. It was pointed at the wrong download server.
As mentioned in the jPortable news story, you should manually download and install the new version.
Sometimes, the impossible can become possible, if you're awesome!