Yeah I can't imagine any call over an hour long NOT having some silence. I've never heard people talk for 1 hour straight without a pause of a minute. In fact, I've probably never heard people talk for 15 minutes without a 1 minute pause in there.
I'm currently single, but when I had a girlfriend, sometimes we had those moments of silence. It's no big deal, like I don't feel uncomfortable. We just spent a few seconds in silence until one of us said something. I only considered it awkward at first when we weren't that comfortable with each other.