You may have a number of issues going on.

First, the final line listing the objects that remain out-of-sync may not be correct.  There was a bug that I discovered yesterday for which a patch is pending, #371, but has not yet been merged.  As a work around run "Scan Link Table" on the kpl_button master object and then restart MH, then run Sync links.  If KPL_button_3 is still acting up, then send the log, or post it somewhere such as pastebin, including the portion where MH tries to sync that device (it is missing in your current log).

Second, if you are trying to create a link from button 3 directly to button 1, you will have to do this manually.  On a KPL, internal links like this are a special beast.  They are not handled by the normal linking database.  I have not gotten around to figuring out how to program these types of links from the software.  Instead, you can go ahead and delete the SCENE_MEMBER link and instead follow the manual process for adding this link.  I believe that this can be done by pressing and holding button 3 for ten seconds and then pressing and holding button 1 until the unit beeps.  You can check your manual for specifics.  MH does not currently know of these links, so you don't have to worry about it being overwritten.

Third, you have some errors in your log that result from trying to treat a remotelinc, remotelinc_button_3, as a responder to a scene, Bedtime_scene.  This won't work.  You need to remove whatever SCENE_MEMBER or _BUILD definition is causing this.

Fourth, this line

01/18/14 12:09:15 PM [Insteon_PLM] WARN: PLM unable to complete requested PLM link table update (update/add controller record) for group: 14 and deviceid: 19f251

Is likely evidence of an issue with a link on your PLM.  Unfortunately the current logging level will not provide us with enough detail to figure it out.  Let's solve your other problems first before tackling this one.