I'm having this issue where I get a pop-up window saying "Android is upgrading..." and "Starting applications..." every time I reboot the phone. It's not the same as when I wipe the dalvik cache where it states "Optimizing applications # through #" for about a minute or two on reboot. What I'm seeing is about 1 to 3 seconds.
I did a complete factory reset, re-flashed the ICS RUU as well as the ROM. It was fine in the beginning and for quite a while after I reinstalled my apps but it eventually came back.
I tried uninstalling apps a few at a time and it didn't change anything until I got down to the last four and then it went away. So, I then tried restoring from nandroid backup and just removing those four apps but it didn't work that time. The issue was unaffected.
I realize that the symptoms point to one or more of my apps but I was wondering if there is some kind of diagnostic logger that I can use to record whats happening during reboot that might offer some hints as to which one(s). One possible indirect culprit might be Superuser. I've had a permanent issue with updating the SU binary. When I do, I lose the ability to add new root apps. I keep root for existing root apps, but SU won't detect any requests from new apps. Therefore, I simply don't update the binary and I have no problems with new apps.
Any suggestions or recommendations would be greatly appreciated.