I'm having the same problem but with a twist. I have my 5 panes arranged just so and when I restart x2 during the same session of Windows, it retains all the pane widths/heights. However, once I reboot my machine and start x2, all the pane widths/heights are changes. This has only been occurring on both my desktop and laptop and only since upgrading to v2.0.
Save program state on exit is enabled. I initially had it set to registry but changed it to file in user appdata folder. This issue occurs with either the registry or file setting.
I use x2 only in maximized mode so I start it and close it in maximized mode.
I close x2 with alt-x or the upper-right X and have verified that the process closes completely each time, especially before restarting my PC/laptop.
I used to regularly export my settings and then when this issue would occur, I would re-import the settings to restore the pane widths/heights but now that I have settings saved in a file, I am not able to export my settings. So this issue is now extra irritating.
Any help would be greatly appreciated.