Hello Alex, I would need to try to replicate this, but I'm not that familiar with mysql to know exactly which folder are you talking about.
What Espionage does is mount the disk image into the folder which you protected, which becomes the mountpoint for the disk image.
Most of the applications accept this and do not bother what is beneath, but there might be some special cases where the app becomes aware that it is not a "real folder".
Maybe the easiest way would be if I can connect to your Mac and we look into this together, I do not guarantee a solution but we can give it a try.
I should be available today whole day, i.e. next 13 hours, for this remote, just mail me at
taoeffect@macmesupport.com.
Rgds
Zsolt