Yet another hopeful attempt at trying to help from me
Those ebooks that you can put through Calibre - how about Converting each of them Epub to Epub and see if they still cause the problems.
So, this means that you will do this Epub to Epub conversion using only the Calibre version of the book (I'm presuming that you've already got those books on Calibre?)
And then, if possible what if you use a brand new Micro SD card to download them to.