Hi Mark,
In the Options, my investments are saved on exit but not my main Portfolio.
So, when I want to reset the setup of my Portfolio to the saved state (in order to close the windows I've opened, etc.), I often just reload the portfolio from the File menu > recent list. This is a quick way to reload, instead of closing totally Fund Manager and restart it. But, in this case, the report windows opened in the previous session remain opened. This is the difference with closing the program and restart. Concerning the graph windows, they are reseted correctly. Perhaps the opened reports should be closed in both cases?