Chrome user-data-dir and profile-directory setting does not store extension preferences

Everytime new chrome version is obtained from chrome for testing, the browser does not remember last settings of our web extensions. It keeps suggesting remove 2 of my web extensions and enable "Developer's mode" for one web extension to run. This breaks our test suite automation. Invoking Chrome with user-data-dir and profile-directory arguments does not help. Is there any way to make Chrome remember last settings for web extension?