1.
If it's a flyback type then you have a transformer in the output stage.
It must be a step-down transformer, right?
With a diode in series? That will create a fraction of a volt drop.
2.
A transformer only conveys AC to the secondary.
So when you say continuous conduction mode, do you mean the transformer primary receives AC with a continual DC component?
Then this is inefficient use of the transformer. Only the AC component will transfer any power.
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Edit: Reading an article I see there is such a thing as using continuous mode in a flyback converter. Unexpected.
I was going to mention that your transformer might be saturating, but I suppose you selected one which can handle the currents you are sending through it, at your stated frequency of 20 kHz.