I also experienced this issue when I had the PHP files that suppose to use SPACES but would use TABS for indentation. Komodo ver. 9.1.3. I transferred settings from Komodo 8.
What helped me is opening the file and going into Edit->Current File Preferences->Editor->Indentation.
Mark Prefer Tab characters over space as ENABLED (was DISABLED originally). Click OK. If you test it, it would be TABBING obviously.
Then again go to Edit->Current File Preferences->Editor->Indentation and uncheck Prefer Tab characters over space. Click OK. Now if you test it you should see SPACES instead of TABS.
The same can be achieved in General Preferences. But for some reason it would not fix the TABBING for all docs in the current project. It would have to be done for each file you open. And then it would save the settings when next time you open it.
I work with files as Projects. I remember Komodo 8 had a preference for Indentation on a project level, but Komodo 9 does not and it seems to be causing some kind of overwriting.
Maybe as Defman suggested removing preferences does help to resolve it on a project level too, but it is a drag to reset since I have made many adjustments for colors and fonts.
I like Komodo 9, but it freezes for me a lot (I am on Yosemite 10.10.5). For example when dealing with saving these TABBING settings and pressing OK, I would have to RELOAD Komodo since the sidebar with the list of my Project files (loaded using SFTP) would stop responding, nothing happens when I click/doubleclick on files. But I am guessing this is a separate issue.
Hope this helps some who do not wish to do the full reset.