Are you using lock screen to hide the "slide to open" slider by any chance? I ran into an issue this morning where, after I had hidden the slider, my icons were jumbled and not even located on screen. It fixed itself once I undid the change.
happened to me many times after installing something new and respringing.
Havent figured out why but the best solution is to use gridlock and iconclasm, and put all the icons close to the top.. it will move them less around
I have been having the same problem. After each respiring, one icon on my homepage would be moved all by itself to a second page, and all the icons on the second page would be moved to the third page, and the third page would become the fourth, etc.
Simply moving the single icon back to the home page fixed everything, but it was still annoying.
A little googling alerted me to IconSupport, a developer app in Cydia. Go to Manage>Settings and choose Developer instead of User or Hacker or it will not turn up in a search.
I installed it and it fixed the issue . It is not advertised as a cure for this issue, and I am certainly not a developer, but again it fixed the issue.
EDIT: I thought IconSupport completely fixed the issue but it still occurs after a new Cydia App is installed. Still much better than after every respiring...