The manual in fact recommends to use the new skies (i.e. the new Time of Day files) only with the included weather patterns. If using different weather patterns, intermittent display issues can occur (e.g sky suddenly changing colour). I have indeed experienced such issues and am now in the process of changing the weather in all old scenarios that I have yet to play to one of the included weather patterns.
Also: @Kim_olesen1 - another update just out:
"Overcast weather at night in Quick Drive fixed"