Never checked it myself, but since I have not seen any reports of it not working for 1.13d and I'm sure a few have updated at this point to 1.13d it might just be your computer. Please tell us the symptoms.
Has ATMA worked on the computer you are using now before you updated?
Which OS are you running? Win7/vista or XP?
Are you getting any errors when you try to run ATMA?
Does GoMule work? If you do not want to install Java I'm not saying you have to, just checking.
You are closing Diablo 2 or at least going to the opening screen before using ATMA. ATMA and Diablo 2 are best run separately so you do not run the risk of duping items. As long as you go back to the screen that has buttons for Single Player and b.net you are safe to run ATMA and transfer items.
You are trying to run ATMA only for Single Player? Just checking since this is your first post. These programs only work in SP never on b.net
Through my experience helping here I have a feeling it is because your computer is running Win7/vista. If you are using Win7/vista your saves are probably in a different area than you think if you are not running Diablo 2 as an administrator.
If you cannot find your saves I suggest doing this: Show hidden files and folders in the folder options dialog box. You may also need to show system folders. Once these box(es) have been checked click Apply and go to this folder. Change Login_Name to what you use when you log into the computer.
C:\Users\Login_Name\AppData\Local\VirtualStore\Pro gram Files (x86)\Diablo II\save
In the folder above are your actual saves. I will not bore you with the details, but suffice it to say it's part of windows protection features introduced in windows vista and continued in win7.
If your saves do not change in the game, try running ATMA as an administrator and see if that helps.
To save yourself the hassle of this windows 'feature' I'd suggest installing Diablo, ATMA and GoMule, if you have it, into another folder than Program Files. Say C:\Games Good luck.
