I hear what you are saying and yes on the surface it does sound a software issue but before you can be certain of this you must make sure there is no hardware issue.

To check that the sd card is sitting properly and is tightly pinned down onto the contacts will cost you no more than a few minutes of your time, if that is ok then you have to check the sd card itself either by the method explained by Retsaw or a similar routine, failing this not being the issue and your sd card checks out ok then what is there left?... your device itself and to put that right, if it was me instead of running around in circles taking up much time and effort i would simply relash both images and start again.

If you have done a backup this does not take long at all in comparison to the amount of time you will spend running routines with no real answers.

All your answers are within this post if you look and get rid of possible causes one by one, you will eventually find your answer.

Good luck it is worth the effort i tell you.