I have a very similar problem with FSC 9.2. I get the message "FSX flight plan folder unspecified! Choose <Flight Simulator X Files> manually." as well. Under load/save I do set it to the correct folder (path tab). Once I switch back to the "LOAD" tab and go back to "Paths" -> same issue. The path will always be reverted to c:\users\my name\Documents.
This is how it looks in the .ini
I have changed it in the ini directly (P:\FlightSimulatorAddOns\FSC9\Flightplan\FSX) -> no effect. Whatever I do, after I close FSC it is always back to FPPATH10=C:\Users\my name\Documents\
The want-have-path exists, checked several times. FSC runs on a secondary LAPTOP with no FSX on it. But there is a symbolic link to FSX, which is also set in the PATHs tab. I am not talking about a shortcut, is is a real symbolic link making the FSX folder appearing as it was locally installed.