I don't see my exact issue here, but I'm new to the forum, so please excuse if it's been addressed!
The TOC's in the ebubs I'm merging are fine - pretty much how I want them. But when I merge them, all the sub-entries are lost, and there's just one entry for each book. I've experimented with the EpubMerge plugin config settings, to no avail.
Here are a couple example files, if I do this right:
http://downloads.30bird.com/xfer/samples.zip
Calibre 2.65.1
EpubMerge 2.0.13