Edited metadata is saved in two places. The PDFE database and the PDF file itself.
When you choose ignore, to face the temporary impossibly to update the file itself (because the PDF reader is not unlocking the file), only the database is updated. That's why you see the metadata locally, PDFE uses the database to show it, but don't show in another instance of PDFE, or in Acrobat, because the new metadata is not in the file.
You may now use the "Update Document Info Fields" batch tool to fix the issue. This batch tool will use the metadata saved in the database and update the file with it.
This problem of Acrobat not unlocking the PDF, even when instructed to load a different file, seems to happen at some systems. Unfortunately can't make it happen here, to better understand the problem.
And indeed, seems that changing the way the reader is loaded, as you mention, sometimes reduces the problem.
Other PDF readers don't seem to have this file lock behavior, so, if using Acrobat is not mandatory, you may try with a different one.