Same issue - same crazy solution - THANKS.
Summary - I have an iPhone 5S and a PC with Internet explorer. Apple will make you believe you can sync your PC bookmarks to the iPhone automatically with iCloud. No matter what you try, this will not work. In fact if you try, you will no longer be able to sync manually. So this fis will let you semi-automatically sync you PC bookmars to your iphone. With the correct settgings (mentioned above), just plug your iPhone into your PC, and the bookmarks update automatically - forget about the iCloud WIFI updating business (I spent hours on the phone with Aplle - ain't gonna happen.
As inidcated above, do two things: 1) on your phone turn off Safari in the iCloud settings; 2) on your PC with your phone plugged in, in iTunes under the info tab, turn on the sync Bookmarks with Internet Explorer. I t will then sync right away, and next time you plug your phone in, it will sync automatically. Good luck