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Assuming that the error is as you describe (i.e. mixture of secure and non-secure items) then yes, the 'secure' items should still have encryption applied - as interzine mentioned, those loaded via http (rather than https) are not encrypted.
However, I don't understand why you'd go to the expense of purchasing an SSL certificate and then not adjust the pages accordingly to ensure the ones you intend to secure are actually presented as such.
I assume that you have some sort of user facing project with this (e.g. ecommerce, login forms or whatever) and therefore the CA issued certificate is primarily for their confidence; you could use a self-signed certificate perfectly well if it's only for your own benefit...
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