Can you make sure that you are using the latest version of the tool. You can use the Check for Updates feature to do this. This latest version included some bug fixes around the area of saved projects, which may help.
The .proj file is simply xml, so you could open it up in a suitable editor and check to see that your settings have been correctly saved. It should be quite straight forward to figure this out. But it you need some help, then please email firstname.lastname@example.org
, quote ticket number F0057735 and include your project file along with an example of one column settings that you are expecting to find.