The most common reason for the series info and collections not being set properly is that metadata management is not set to automatic. But, as you have checked this and the driver configuration, there is something else happening.
As you are using the KoboTouchExtended driver, are you configuring the correct driver? While the function that is not working is supplied by the main KoboTouch driver, their configuration is separate and the one in used has to be configured.
Beyond that, I need to see a debug log. Run calibre in debug mode (right-click the preferences button and select "Restart in debug mode") and connected the device. When the connection jobs have finished, close calibre and the debug log will be displayed. Post the full comments, or PM it to me, and I will have a look. I can usually see what is going wrong.
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