The shortcut to reset to saved layout (Shift + Opt/Alt + 0) resets the layout, but pops out the project panel into a seperate window every time. I was able to temporarily resolve this issue by creating a duplicate copy of a preset layout, however, the problem affected my custom workspaces after I shut the program down and started it back again.
Clicking "Reset to saved layout" from the Window menu or from the Workspace shortcut menu does not experience the same problem (hence the bug report.)