JCalibre got me an example.
What's happening here is that the second of the source epubs is an epub3. EpubMerge automatically converts to epub2 using Calibre Convert before merging.
In this case, the conversion is what's changing the CSS. Calibre's Convert significantly rewrites basically everything because internally it first converts to a common format/structure before outputting the selected format.
At this time, I don't have any easy fix for you. In your shoes, I'd just try to fix up the output file, or convert the 2nd input to epub2 myself and fix that up before merging.
I have been (and continue to be) reluctant to try and support epub3 natively in EpubMerge. Epub2 Table of Contents is relatively consistent. Epub3 ToC is just an HTML5 file. Could be <ol> lists, could be nested <div> tags, who knows. And that's just a lot harder to deal with.