Tests for infectious diseases, in general, are incomplete. Even if the antibodies to that particular virus were not high enough that the doctors think of it as a cause, it is possible that there was another infection that didn't show up on the tests, because the particular strain wasn't tested for, or because the test wasn't sufficiently accurate. Some infectious diseases are difficult to test for.

So I wouldn't rule that explanation out.

One thing you could do is do more wide ranging tests for infectious diseases by testing for their antibodies, and also you could test for cytokines (eg. interleukins) which are markers of inflammation in the body. If some of the cytokines are high then that would be an indication of an undiagnosed infection, or another cause of inflammation. Then you could look into it more, and potentially treat the infection before starting to seek another pregnancy.

Garth Nicholson, a professor and a founder of an institute has recommendations for which labs have good tests: http://www.immed.org/clinical%20testing/ClinicalTesting2015.pdf

As of 2015, he is recommending

Clongen Laboratories http://www.clongen.com

Igenex http://www.igenex.com

for infectious diseases.

He used to recommend RedLab for cytokines, but they went out of business. I'm not sure who is doing high quality cytokine testing these days. And there aren't very many people around who would be helpful in interpreting the results, since cytokines are relatively new as biomarkers. But cytokine testing can indicate problems that other tests miss.

Nicholson's perspective on chronic diseases is not shared by many doctors, so you'd have to evaluate his ideas for yourself, but I have respect for him. He has a PhD in Biochemistry, and has published hundreds of scientific papers.

An infection may not have been the cause of the problem at all, but if you want to explore it more, that's what I would suggest.