I have tried this and could not replicate the problem as such. I have noted this to be confusing settings rather. In this case I think you have forgotten to set the Default Theme in the "General Settings" ui. To resolve this I have improved the Theme Manager to better handle theme assignment and set default themes also for general settings preventing confusion.
As a note, remember to update the include path for your custom theme.
I have tried this and could not replicate the problem as such. I have noted this to be confusing settings rather. In this case I think you have forgotten to set the Default Theme in the "General Settings" ui. To resolve this I have improved the Theme Manager to better handle theme assignment and set default themes also for general settings preventing confusion.
As a note, remember to update the include path for your custom theme.