Hello...
I have no clue if this will help you or not but I thought I'd at least try.
I tend to use the "List" view most of the time so I, too, had to update my settings to adapt to this change. Also, since I've chosen not to hide system files, I added all "desktop.ini" files to the "Hide Filter" section in the "Filters" tab via the "Folder Options" settings. For whatever reason, I hated seeing those files all the time. 
There's a few things I did to make sure Dopus started - or opened new tabs - in the proper customized view. I'll list them for you but, keep in mind, I'm going by memory right now so I may miss something - and - you may already know this info. With that in mind:
[ul]
* In "Folder Options", I updated the settings the way I wanted them and then selected "Save" followed by "For this folder and all sub-folders."
[ul]Note: Since I use the Dual Display mode (2 listers), I finally figured out that I had to make the same change for both listers within the "Folder Options" area. Prior to that, I was only seeing my changes in one lister.[/ul]
* Once that was done, I added a couple more tabs to each lister (for a total of 3 tabs in each lister) so my most-used directories were always just a click away in a separate tab. Once I had the correct directories opened in each tab, I saved them as a "Folder Tab Group" so I could open all 3 tabs in one click when/if needed.
[ul]Note: In my setup, these tabs are visible immediately upon starting Dopus. That's because I used the "Save Layout" feature described next.[/ul]
* After making changes to the "Folder Options" settings, and creating my custom "Folder Tab Group", I navigated to "Settings > Lister Layouts > Save All Listers" and saved my entire configuration as a custom layout.
* From there, I navigated to the "Preferences" screen, followed by "Launching Opus" and "Startup." I changed the drop-down in the "Open a saved lister layout" setting to reflect the custom layout I created in the last step. That way, whenever I open Dopus, I know all my settings/preferences/tabs, etc. will be loaded.
[ul]Note: Since I usually leave Dopus open throughout the day, I also changed the setting found in "Launching Opus > From the Taskbar icon" to "Bring the last active Lister to the front (new Default Lister if no Listers open).[/ul]
[/ul]
Now - whether or not this info has anything to do with your issue, I don't know. I just thought I'd put it out here in case it helped in some small way. Other than what's mentioned above, the only other items I can think of would be:
* Remember that any changes made in the "Folder Options" area need to be made to all open listers (not all tabs - just listers) in order for them to take effect in each one. You must save the changes for the current folder and all sub-folders in each lister. If you're not using a dual lister display - or several individual listers at the same time - then this may not apply to you.
* Remember to save your layout under "Settings > Lister Layouts > Save All Listers (or Save This Lister)" to retain your settings going forward.
* Ensure "Ignore folder format of Default Lister" isn't checked in "Preferences > Listers > Options > Default Lister." It's been so long since I made these changes that I don't recall if this option is selected by default or not. It may, or may not, have an impact on your problem.
* Look through your "Preferences" settings again as it seems like there's something creating a conflict with your changes. It took me a while to get things right. Prior to that, I experienced similar inconveniences, too.
* BACK UP your settings and layouts once you've got them just right via the "Settings > Backup & Restore" option. You may want to back up your File Types settings when/if you make changes as well via "Settings > File Types > File > Export." I'm a fan of backing up data if you can't already tell. 
Good luck with getting your issue sorted out for good. I hope this info helps you along the way. If not, oh well. I tried, right? 
