To reproduce, add an EEP or Day Cycle to your land with the Cloud Scroll on Y Axis set to 0. For some reason whenever the Y Axis is set to 0, it will stop the clouds even though X axis has a number. I've reproduced this bug by testing it extensively. When X axis is 0 and Y has something, loading the EEP and Day cycle works, but when Y is 0, it will immediately stop the clouds and you can see this by going to CUSTOMIZE and editing any points on the timeline, suddenly both X and Y Axis points are zeroed out.
