Alex, I thought it's related to skins cause that's how I got the error, then I tried a simpler scenario without changing skins and the bug appeared again. Here's the scenario:
1-add an HTML module to a page
2- from module settings, check "Display Module on All Pages", then update. (Now the module display on all pages, as expected)
3-from module settings, UNcheck "Display Module on All Pages", then update (Now the module display only on that page, as expected)
4-from module settings, check "Display Module on All Pages", then update
Now the module should display on all pages; but it doesn't. it appears only on the originl page.
It has something to do with the new "Add to new pages only" setting, cause the module above gets added to new pages! What happens is that in step 4, "Add to new pages only" is set to true without the user choosing that.