BossPaper v1.1.1 is going into Cydia now. It’s a bug-fix release only. I hope it solves all the issues that some people experienced on v1.0, although I cant be sure as I cannot reproduce any of the missing icon issues. In any event, the changes are:
1) Fixed background location to include statusbar again.
2) Fixed help screen to talk about how to use the new “Under Winterboard” feature. See Help, then Feature Description.
3) Made some changes internally to try to make things more like how 1.0 worked for those that were having problems with layering when using winterboard. I verified this fixed the problem for one person, (thank you Scott). I still cannot reproduce this issue so can only hope for the best.
4) The change to #3 above also impacted dimming if you had a winterboard theme behind the bosspaper. On v1.0 the winterboard theme was covered but on 1.1 the paper dimming let the theme show from behind it.
If anyone is still experiencing the missing icons issue, I need someone that is SSH savvy to help me debug it further or anyone that can give me enough details to reproduce it on my own (a complete list of your winterboard themes and which ones are applied and in what order for example, also disable all winterboard themes and test, etc).