Remember Pinned Windows not working as expected

[Lothex91]

Using the "Remember Pinned Windows" checkbox from the Window Controls module gives a strange result: when the program is closed, next time it is opened the pinned window is opened again, but this time there is an x to close the window, whereas when it is pinned there is no close button. So it looks as if the window isn't pinned. Yet, if the program is closed and reopened, the window reopens normally.
It may be an issue with PDFoundry.
EDIT: I double checked, it is an issue with PDFoundry, because journals work as expected.
Only PDF Windows work as described above.