I think it was the CR/LF stuff. And indeed I was so stupid to ignore the warnings.

However, it may also be related to the Mass set tags/flags -> MP3 flags to set -> Whole file option. This option caused a lot of [censored] when I tried to use it. It corrupted some files straightforward and hang my system a couple of times. Are there any known issues with this option? If I am the only one having issues with this option it might be my system + the CR/LF thing.