Hi Matthew
Unless those domains had particular bad link profiles or indeed had a penalty put on them, then I think you're right and we can rule out that reason.
I'd first check webmaster tools and see if there are any large crawl errors - you basically want to make sure that all of the pages on the site are accessible by Google, all of the links pointing to the site are working (or redirected to a working URL) and that your 404 page is working (and not returning soft 404s). Should you find something irregular here, that's where I'd start ASAP.
I'm guessing one of these domains was the old website URL? In this case (and apologies if this sounds obvious and you've already done this) I'd double check the 301 redirect has worked properly, so that all the old links pointing to the website are now.
Now, as for the rankings that have dropped - are they across the board and for all keywords, or are they limited to specific keyword groups or specific landing pages? Depending what the result is here this could mean a number of things. When you did the 301 redirect, did you redirect the URLs to the equivalent pages on the new domain, or all to the homepage? If its the latter, is there a chance that the links you were pointing to the old site are now not "powering" the equivalent pages on the new site, as they're going to the homepage?
Similarly, if the rankings that have dropped all go to the same landing page, then there could be a problem on-site or off-site with that page. On-site, Google might not think the new page is very useful to the reader if there is not a lot of content it can crawl and read. Off-site, the algorithm may have devalued some old links to that page if it thinks they are not useful/editorial, such as old directory listings or article site links.
If the drop is across the board, for a number of keywords and landing pages, it could indicate a penalty of sorts, so I would check your webmaster tool messages for any link warnings.
If there's no warnings there, nothing out of the ordinary in terms of errors and your confident that your links are editorial and authoritativ and so would not have had a bunch of links devalued, then I would call for a bit of patience to see if things recover. After all, the Googlebot is going through a bunch of new pages and might have freaked out a little bit - but hopefully I've provided a few things to check in the meantime, in case the drop becomes sustained.
Hope this helps Matthew, wish I could be more of a help.