As described on forum: http://forum.kerbalspaceprogram.com/index.php?/topic/149733-122-environmentalvisualenhancements-12-2/&do=findComment&comment=3027031
For reproduction:

1. Install KSP (version 1.2.2)
2. Add this Mod, its Default Configuration, and HaystackContinued (https://github.com/qberticus/HaystackContinued/releases/tag/0.5.2.1)
3. Launch new game
4. Build and launch a new rocket to orbit - the clouds will look as beautiful as expected
5. Jump back to the Space Center
6. Jump back to the ship in orbit using the Haystack Continued Menu - do NOT go through the tracking station
7. The shadows of the clouds on Kerbin won't match the clouds and the clouds move strangely, especially during time warp