Will a graduate student publishing in different disciplines confuse potential employers? I'm a third-year computer engineering PhD student. My dissertation topic is re-configurable caches (computer architecture) and my supervisor is a very nice person. I have four publications with him in well-known conferences in my area. But currently I'm in a weird situation. In my 2nd year I fell in love with computational neuroscience and started working on it with another professor in my university simultaneously with my PhD research. Obviously my PhD supervisor encouraged me. Recently I got two high-impact journal publications as a first author on cognitive neuroscience. I am very happy with my dissertation topic but also want to include my neuroscience papers in my résumé. I would like to try for faculty positions after the PhD. Do you think my résumé can create confusion among potential recruiters or will it show multidisciplinary research interests?
The only real danger you will have with prospective employers (presuming that you look for a postdoc before your faculty search) is that a potential advisor might be concerned that if you aren't engrossed in their research, you will seek out opportunities in other areas. If it's their money that's supporting your time, then you'd be expected to devote your effort to the line of research you've been hired to do, not what you'd like to do.

This is something that you'd have to explain in your cover letter in any case. But you'll need to explain—as you have—that your lateral move was encouraged and done with the support of your current advisor. Otherwise, it could be a concern.