When evad3rs had pushed fixes for long reboot and weather application crash issues, it was imminent that they would also implement them on their tool called evasi0n. Since its release, this is the second version of evasi0n which would fix the same issues that are meant to be fixed by evasi0n iOS 6.0-6.1 untether and UIKit Tools in Cydia. This means that you would not need to install these updates every time from Cydia when you are finished JailBreaking your iOS device.
But now, all you need to do is to run the evasi0n 1.1 on your iOS device, and these issues would automatically be taken care of. If you want to fix these issues manually, you could even do it with the help of either replacing the mobile.installation.plist or force reboot. According to iOS hackers, the weather app issue arises due to the interruption of App Sync which is a patch used to install pirated apps.
Therefore, if you are still facing these issues, try uninstalling App Sync from Cydia, do a reboot and the issue would be fixed in most of the cases. Let’s know in comment section if you are repeatedly encountering them even though you deleted App Sync previously.