For what it's worth: I had the exact same issue. Graphics errors in the skybox. CKAN showed an incompability between PS and ALA, but only Planetside always threw an error message when I tried to uninstall. The Mod still showed up in CKAN after I manually deleted the folder, and any click on "uninstall" crashed CKAN. And since I could hence not get rid of the graphic errors in the skybox, I did a fresh install of KSP and skipped the (still very nice) Ambient Light Adjustment Mod. Everything fine ever since.
However nice CKAN is for convenience (and I appreciate it very much in this regard, running ~50 Mods peacefully in perfect harmony currently), I got a vague feeling that a complete reinstall would perhaps not have been necessary had I gone without CKAN (but perhaps those two Mods would have corrupted my game on their own even without CKAN, so who knows...)
