The nether dust continue even when overworld rain stopped or if the player try to desctivate it with the weather clear command. The only way to stop it to get out of the nether and come back, and sometimes it doesn't work, obliged to reload the world.

In vanilla the dimensions have their own sets of timers for rain duration and what not. I will have to take a look to see if things are working as intended. Question: when you ran the /weather clear command were you in the nether or overworld? If not in the nether have you tried running it in the nether? (Again, the weather system in the alternate dimensions are kinda separate based on my recollection.)

Just looked at the code. Something changed in the underlying Forge/Vanilla implementation. Oh joy! This one is going to be fun.

Sorry my bad. My world was a bit corrupt from all the gyrations. The rain duration timers are separate for each dimension so the situation you outline above is possible.

I did find a bug related to nether and when the effects actually show in the client. This fix will be in the next BETA. It could be the cause of what you are describing.

EDIT: And it only applies to the 1.11.x version of DS, which is what you are using if I recall.

Pushed a v3.4.3.0 version with this fix.