I had same problem but resolved it like this:
1- Open Nautilus in root mod via
2- Go to \home\username\FlashTool then delete all file of FlashTool folder
3- Download FlashTool 0.9.11.0 HERE then FlashTool 0.9.16.0 HERE
4- Go to Oracle site to download Java 64 Bits HERE
5- Always in root mod in Nautilus go to /usr/local then copy the tar gz file of Java 64 bits then uncompressed it in folder.
6- Once the file uncompressed right click on folder of Java folder and copy to to placed Java Folder in FlashTool folder.
7- Reinstall FlashTool files of 0.9.11.0 version in FlashTool Folder then make the same for FlashTool 0.9.16.0
If all works you will be able to launch the new version.
for me it works