I have done the following and couldn't reproduce any problem in r59:
- opened an existing .capx
- added an animation frame to a sprite
- saved as project folder (and a second time around saved to a .capx)
It worked fine both ways. I haven't yet checked out the more detailed instructions in your PM and will do soon. I did warn about possible issues in the r59 changelog so do keep backups! I'll try and get this properly sorted with a new release out before the end of the week.