I use Altium Designer 18. When I open a project file (.PrjPCB), the asterisk ("*") appears next to the project name indicating that the project has been modified, but I haven't actually made any changes.
I've been using Altium for years, and I've always wondered about this. I'd really like to change this if possible, because I sometimes worry that I've somehow accidentally made changes to the project that I didn't intend.
EDIT: I'm aware that in some cases, Altium can't find the library files that are linked to the project and removes those from the project. This is not what's happening in this case. Often, when I open a project, and no library files are removed from the project, the project is still modified and (even if I don't make any changes), I'm asked if I want to save changes to the project when I close Altium.
Also am not making changes to any of the project files (.SchDoc files, .PcbDoc files, etc).
Best Answer
It might be saving your project state (i.e. previous view/zoom and currently opened files in your project). I know several programs that do this including schematic capture, PCB layout, mechanical CAD, IDEs, and even spreadsheet software that liked to save which cells you were looking at and which cell your selector was on.