Yes, it is clearly a calibre issue. Which is why@pdurrant pointed you to a thread discussing the problem you were having. It turned out the problem wasn't actually in the plugin the thread is for, but, it's understandable why people reported it there. Add to it that the extended driver and the Kepub Output plugin share a lot of code, there is a high chance that any problem for one, is also a problem with another.
But, the problem wasn't in either, it was actually in the Kepub Metadata writer plugin. The last release of this plugin was broken when writing the OPF file. It usually ended up as zero bytes. There was another problem in the extended driver and the output plugin that has been fixed. There was a release of all three plugins about two hours before your post that fixed these problems.
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