The issues you are having are caused by some underlying differences in the flex libraries in EB 3.4 and 4.5. Using EB 4.5 allows using flex spark components however these are not backward compatible to CS 5.5. In order to have an extension that is backwards compatible to CS 5.5 we strongly advise using EB 3.4. That does unfortunately mean that you will not be able to use the design view. The AutoTheme library was created to provide the theme syncing ability that is available in EB 4.5 through the "CSInterface.instance.autoThemeColorChange = true; call to EB 3.4 extensions and does not work with EB 4.5 (as you have found) because it is trying to set the theme of a different set of UI components which are not available in EB 4.5.
So to summarize:
AutoTheme.sync() is what you should use for EB 3.4
"CSInterface.instance.autoThemeColorChange = true; should be used with EB 4.5
they provide equivalent functionality and should not be mixed.
Finally we would strongly advise using EB 3.4 for CS5.5 extensions.
For the combo box issue unfortunately we only had the capacity to create a broad theme that should cover the majority of the controls correctly, however some controls are not ideally themed. However we do provide AutoTheme.postThemeColorChange which can be set a function to run immediately following theme setting that should allow you to customize the theme to cover these cases.
I hope that helps,
Thank you for your response - I feel I understand it a little better now!