I did a search for this issue but didn't come across anything specific, please point me in the right direction if this is already addressed.
I noticed that there is a difference in the way server and desktop sort folders that start with a tilde. In desktop, a folder with a preceeding tilde is sorted at the bottom of the folder list and in Server it's pushed to the top.
Also, this is happening within a published data source.
On Server, the folder '~Other' gets listed first in the folder list
On Desktop, the folder '~Other' gets listed last in the folder list
Is this a known issue? Is there a character encoding difference between the two?
It's an interesting observation, I tried it out and get the same results as you. If it's important enough (for you), you should open up a case with support. Or you could just use a different special character such as "_"