In version 2.9.9.8 Beta (984254) 64-bit on Windows 10 Home version 1903 O.S. build 18362.959, the compile window does not retain the selection for front matter.
Specifically, when compiling for PDF, using a modified Manuscript format, I check the “Add front matter” box and select the folder Manuscript Format , It compiles correctly. But when I try to compile again (later in the same session or after exiting the program and restarting it), the checkbox remains checked but the selection reverts to none. This behavior occurs regardless of whether the lock icon is locked or unlocked.