Interesting link, no answers yet. Please keep us informed!
You may still try running simple applications written in languages C and Java (also BAT, Vbscript) on the vulnerable station. If you want my help here, please contact me privately. I'm interested in the cause and solution for this problem.
Modulok, I still have no idea what causes unwanted behaviour in your installation. But I have some more thoughts:
1. rm a; touch a - preserves the inode, while you seem to think that is changes it
2. Please try to run the following macro. It basically does what save does, but it's code is absolutely clean. Test how does it affect the permissions. The next step could be to write a simple java...
I tried to reproduce but failed. My steps:
1. starting clean jedit 5 with new settings dir (-settings=a_non_exist_dir). I also have Win7 64 jre 1.6.30
2. prepare the file on samba share (debian)
3. checked 777 - ok
4. edited - yes, file spoiled, because of 2-stage save; however I got -rwxrw-rw-
5. turned off 2-stage
6. works ok, preserves 777
7. tried different backup settings and...