When you open a file in a project and then close it the Package Explorer will scroll to a file in another project if there is a file open there. Is there a way to stop this behaviour?
It sounds like you have the 'Link with Editor' option toggled on. This links the Package Explorer and the editor, which can cause the behavior you are seeing.
This option shows up in the Package Explorer header area as a button with arrows pointing right and left - if you hover over it, it'll say 'Link with Editor'. Click it once to turn it off, and it should stop automatically scrolling the Package Explorer view.