I have noticed that after a site is published, if you make updates to the project and republish, that all files are republished (especially after you have closed Elements and then return on another day to make updates).
Also, if you want to re-publish just a single page it does not work.
I have only got one project at this time that is live so I can’t say if this is a general thing or just on one project. Will be able to say next week 
Yes, the publishing manifest currently resets between launches… it’s a known issue, and we understand how frustrating that can be 
The good news is we’re planning a full overhaul of publishing soon, and we expect that to resolve this and other related quirks 
Thanks for your patience in the meantime. it’s appreciated. Stay tuned!
@dan Hopefully as part of the overhaul you will also look into ensuring that all connections to the server are released after publishing. Often if you do a publish shortly after performing one you will only get 2 connections (instead of 6) because the previous 6 were not released and the server only allows 8, so you are stuck with 2. Classic was notorious for this problem, so I was surprised to see it surface in Elements. It can be frustrating.
My workaround is to quit Elements for a few minutes and then relaunch it. This gets the connections released so you can go full speed ahead with the next publish.
Cool thanks @dan