so many posts on this thread and i am not sure if someone else noticed this but here goes and i hope this helps other people ...

I copied the data files from my windows box to the n900 using openssh (I have the steam version of JA2).
Did all the root access stuff etc.
But I was having problems with the data files even after editing the .ini file.
I kept getting the error message when running the shortcut saying it could not locate the data files.

So i loaded up X terminal and started it using ja2.
I would get an error message 'failed to open "/home/users/.ja2/Data/data.slf"
I checked the directory and the file was where it was ment to be.
But i remembered that linux is fussy with UPPER and lower case file names.
All the files in the data folder have UPPER case letters at the start.
So i renamed the Data.slf to data.slf
Then run ja2 from X termal.
After doing that i would get a diffrent error message saying that i could not find ambient.slf.

Anyway so let that be a lesson to you and make sure that WinSCP is setup to copy files in lower case!