I've noticed these same messages for a long time now. I only noticed them because I was troubleshooting my audio issues with Media Center and I went looking in the Console for any possible clues.
I don't have any "double icon" behavior. I'm not even sure what that is. I *think* these messages are just informational, as opposed to "this is broken!". The programmers will ultimately have to decided if they are a problem, or just extra information. Just to be complete, here's a sample from my system:
7/23/15 1:49:37.387 AM Media Center 20[38488]: objc[38488]: Class JRWebView is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libdsp_Main.dylib. One of the two will be used. Which one is undefined.
7/23/15 1:49:37.388 AM Media Center 20[38488]: objc[38488]: Class JRNSView is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libdsp_Main.dylib. One of the two will be used. Which one is undefined.
7/23/15 1:49:37.388 AM Media Center 20[38488]: objc[38488]: Class JRNSWindow is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libdsp_Main.dylib. One of the two will be used. Which one is undefined.
7/23/15 1:49:37.393 AM Media Center 20[38488]: objc[38488]: Class JRNSWindowDelegate is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libin_FLAC.dylib. One of the two will be used. Which one is undefined.
7/23/15 1:49:37.393 AM Media Center 20[38488]: objc[38488]: Class JRWebView is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libin_FLAC.dylib. One of the two will be used. Which one is undefined.
7/23/15 1:49:37.393 AM Media Center 20[38488]: objc[38488]: Class JRNSView is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libin_FLAC.dylib. One of the two will be used. Which one is undefined.
7/23/15 1:49:37.393 AM Media Center 20[38488]: objc[38488]: Class JRNSWindow is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libin_FLAC.dylib. One of the two will be used. Which one is undefined.
7/23/15 1:49:37.393 AM Media Center 20[38488]: objc[38488]: Class JRCmdRelay is implemented in both /Applications/Media Center 20.app/Contents/MacOS/Media Center 20 and /Applications/Media Center 20.app/Contents/MacOS/Plugins/libin_FLAC.dylib. One of the two will be used. Which one is undefined.
If you need more, I can paste more. The forum stopped me from pasting a bunch at once (character limit exceeded).
Brian