Trouble using Time Machine with SMB share in OSX El Capitan

This is going to be a throughly unsatisfying answer, but it comes down to the fact that random network drives were not meant to be used as time machine backup targets.

I'd wager one of the things you did in your guide was to run a terminal command along the lines of:

defaults write com.apple.systempreferences TMShowUnsupportedNetworkVolumes 1

Unsupported being the watchword here.

I've run into this exact problem myself, but only when backing up to network shares.

Usually what it takes to break Time Machine out of its funk is to completely disable it (toggling the switch to off in the preferences pane), unmount your network share, remount it, and then re-enable time machine. The system is smart enough to see that you already have backups in the bundle file and you won't lose any data.

Still - you're playing with your safety net. If the contents of your machine are super important, please pick up a time capsule so you don't wind up with a nasty surprise some day.

I've no idea what triggers this behavior - it appears to be completely random.

In case you haven't found a solution yet, in the guide I was following it never mentioned to run the tmutil utility to set the backup drive via command shell, so just run the following command on a Terminal and you will have the disk selected on Time Machine Preferences:

sudo tmutil -a setdestination "/Volumes/Time Machine Backups/"

Remember to change the name of the volume, in my case as I used makeImage.sh it defaults to "Time Machine Backups"