I would not recommend trying to do a distribution upgrade via the stats page; ssh in and do it directly. I have actually disabled some of those commands for exactly this reason (but it is not live until next week)
Getting an automated wheezy to jessie upgrade right is tricky at best, and basically impossible when there are user modifications to contend with, so we don’t try because it’ll break stuff if it goes wrong. The piaware/dump1090 upgrade touches only the piaware and dump1090 packages. If you want to upgrade the whole system to jessie, you’ll either need to shepherd the distribution upgrade yourself, or reimage with a 3.x sdcard image.
Starting with a clean image is the recommended way to move to Jessie. If you really need to update a Wheezy image, we have tried an unsupported upgrade path which is documented on the forums here. This has been shown to work on a vanilla Wheezy image, but we can’t predict what effect it may have on any packages or data that you have installed, so this is very much at your own risk. Feel free to add your experiences and improvements to the upgrade process to the forum so others can benefit.