I have this wierdness. Every once in a while my tray icons disappear after a soft reset. It sometimes takes a couple of resets to bring them back. I am using Pocket Informant, with Pocket Breeze, and Pocket Weather running on my Today screen. iLauncher is running in a tab in PB.
I also run vjtoggletoday, wmnewmenu and vbar
Normally, the BT and wireless are visable, and when I load ilauncher I get the ilauncher tray icons for psSHutXP, activesync and ilauncher settings. As you can see in the attached photos, I don't have the tray when it reset, nor do I have them when I call ilauncher in the tab. Anybody have any ideas