The problem: When I log in to Netrunner, there are no icons on the desktop, using the “Netrunner Desktop” view. Right-clicking on the desktop, changing the view to something else (e.g. “Default Desktop” view), then changing it back to “Netrunner Desktop” view, brings the desktop icons back.
I have the same Issue. 9 times out of 10 Netrunner boots with all the icons on the desktop, and lately I only have 1 to 3 icons on there, and that occasional boot they will be missing. When this happens I am left with a little square drawn in the upper right corner of the desktop which does nothing but highlight when I click on it. The icons do not come back with a desktop refresh, but they do come back after a reboot. Before, when I had a few more icons in a vertical column on the left Netrunner would occasionally split the desktop in half horizontally and give me a scroll bar on the right on the upper portion to scroll to my icons further down. It still displayed the desktop background properly in this case. Again, things are normal after a reboot. Both cases have happened to me several times on 13.06 and 13.12. It is not life threatening but it seems annoying or unstable for this to happen.
You are probably right, as the solution recommended in comment #314 in that bug thread seems to offer a permanent fix. That is, to resize the bottom panel so that its edges don’t extend to 100% of the screen width. Just a little bit of a reduction works, and the icons no longer disappear.