studeo,
I haven't determined if you are using your own "hand coded" version of the code for Google Analytics tracking, or are you using the Contribution available in the downloads section?
If you are using the Contribution, then it already accounts for SSL vs. non-SSL connections.
If however you are using a "hand coded" version (your own) to track Google Analytics, then you will have to account for the SSL vs. non-SSL versions.
I presented code in an earlier post (you'll have to go back a ways) that did just that.
To answer your question, yes, I have it working on SSL and Non-SSL sites just fine (and switching between with no problem).
It may be that the issue in your case is not related. Are you sure you have the tracking installed correctly (from the beginning)?
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