Thanks for your reply William.
According to the Klipsch website (http://www.klipsch.com/na-en/products/hd-theater-1000-specifications/) the speakers are 8ohms so I'm not sure that I should change the receiver to 4ohm setting.
To clarify the problem it didn't start immediately when I hooked up the new speakers almost 2 weeks ago now, the first time I noticed it was this past Monday (about 8 days after initial purchase and set-up) when I started the system and only the rear L surround and subwoofer were playing, and then one by one (several minutes inbetween) the rest started to work and it was fine. The very next day I turned everything on and all the speakers worked except 2, which similarly started to play after several minutes. Wednesday they all worked right away when I got home, and yesterday only one didn't work (but did again after waiting for several minutes), today they all worked immediately again with no issues. This is the most detail I can give, unfortunately I don't know nearly as much about the technical workings of these electronics to identify the problem.
It's quite annoying to not be sure when I'm going to have to wait for the system to work, kind of like having an extremely slow pc where you plan to boot it up about 15 minutes before you actually want to use it.
The idea of the factory setting reset is really good and I think I'll try that this weekend. Thanks again for your response and insightful advice.