If you are using Acrobat as the PDFE internal PDF reader, this is a problem that seems to happen at some systems because Acrobat don't close the previously open PDF, even after new file charged. I never experienced this problem, so never got a chance to debug it to try to understand why it only happens sometimes, and just in some scenarios. You can easily check if this is what is happening at your system, if you can successfully update the metadata for a not open PDF. Just edit the PDF metadata without open it in the PDFE PDF view.
Try changing the way PDFE uses Acrobat, under menu Edit>Preferences>InternalPDFReader. Change from "Internet Explorer Default", to "Adobe Acrobat".
But what I really recommend is the use of the free Foxit PDF Reader or the PDF XChange Viewer, instead of the not easy to control, and resource hungry, Acrobat. Just install one of those, make it the default system PDF reader, and make sure PDFE InternalPDFReader option is set to "Internet Explorer Default".
