@jangell2,
Can you make sure you are using Calibre 0.7.56 - there were some issues in 0.7.55 that may or may not be related and its best to make sure we're using the same version to test. And version 1.5.3 of the plugin which you said you were using (can you recheck in the Preferences->Plugins->User Interface list. I'll add the version # back to the reports for the next release).
If its still not working, can you attach your debug output (to use debug, see Troubleshooting in the first post) - if you don't want to post all of your book details, then PM me with the information.
There are a couple ways the plugin can be used. Assuming you don't want to use Edit Collections to manually maintain your collections, then you want to use Create Collections: 1) Use Customization to select (change action to 'Create') the columns you want to use when automatically generating collection names, 2) run Preview Collections to check the output, 3) run Create Collections to create them on your Kindle.
Now, if you already have collections on your Kindle, you can run Import Collections to import all the names into a custom column. You can then change Customization to select that custom column, and then run Preview/Create, and the collections will be recreated based on the columns you selected. You can select multiple columns in Customization - so you can select your custom column and add all Series names for instance.
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