OmniOutliner 3.9 beta 3 is now available! There's a lot of small fixes and features in this release. Most notably, the issues with AppleScripts on the toolbar should be fully fixed now and alternate row color is now supported in DHTML and Quick Look. There's also been more work on the docx export. InDesign and OpenOffice should no longer crash when trying to import the docx files. Please read the release notes for full details.
The issue with the software updater leaving the old version behind when not asked for should be resolved as well. You will still see this issue when updating to beta 3 though since the fix won't take effect until you're updating from beta 3.
As always, please let us know if you run into any problems by using the Send Feedback option under the Help menu in the app or by sending an email to firstname.lastname@example.org. If you're ready to give it a go, head over to the download page or use the updater in the app!