For the past few days after doing the 6.1.1 update and jailbreak, these empty white boxes have been showing up on my phone. I have to reset to get them to go away. Any idea what is going on?
It happened to a lot of people at this jailbreak and after the ios5 jailbreak.
I don't know that the source was ever determined.
I know for me it eventually just stopped. But your handling it right, a respring also solves the issue
No need to panic. These are first party apps that aren't supposed to be used by consumers. As you've already discovered a simple respring will hide them. Personally I get them only when I start installing and deleting tweaks from Cydia. Once I get to my ideal setup I forget they exist.