If you are continuing to experience the same problems please can we ask you to try the following suggestions:
Just purchased powersaves with the purpose of backing up the save data for my Pokemon Y game, now my question is, where does powersaves backup my file to? I can't find it on the installation folder, so I assume it places it somewhere else. To copy them to the PowerSaves directory, go into the folder containing all of the BIN files. Hold Shift and right click (on a blank space, not on a file). Click 'Open Command Window Here'. Now enter the following EXACTLY the while you see it.
Please ensure that you are running the latest PowerSaves 3DS software
We would recommend using a different USB cable with the PowerSaves 3DS transfer dock.
Please try configuring or temporarily disabling your firewall software or any similar software to allow the PowerSaves 3DS software access to the internet. If this resolved the situation then please update your firewall rules.
Please try using a different computer to confirm if the problems which you are experiencing are limited to your computer setup.
If you continue to experience the same problems after following the above suggestions, please can we ask you to answer the following questions in your support request to enable us to advise you further:
Please can you provide your PowerSaves 3DS license key and the registered email address.
Please can you detail the messages reported by the PowerSaves 3DS software when inserting your 3DS game cartridges.
Please confirm the 3DS game cartridges which you are inserting in to the PowerSaves 3DS transfer dock
Please can you confirm the version numbers from the front of these 3DS game cartridges, for example LNA-CTR-EKJE-USA.
Please can you confirm the version of Windows which you are using for example Windows 7 64bit.
Please can you confirm if you were able to try using a different computer and if the computers share the same internet connection.
Please can you confirm if known the type of internet connection in use or your internet provider.
Please confirm that the registered email address and license key are correctly entered within the PowerSaves 3DS software options screen
1. Make a save backup of your game for the cartridge you want to use and then copy the Save out of the Powersaves folder to a place like your desktop for safe keeping while keeping a copy in the Powersaves folder.
2. Download the tool on this page found in swarzesherz's post: http://projectpokemon.org/forums/showthread.php?37269-X-Y-Save-File-Research/page5
Mac Open Bin File
3. Open the program and select your save in the Powersaves folder by selecting Open Save 1 button. Then hit the Clean Save 1 button and select the Save in the Powersaves folder so that it overwrites it.4. Restore this save to your cartridge and then go in game to the language select screen, at the language select press the Home Menu button and close your game while not hitting any other buttons.
5. Place your cart back into the Powersaves and then use the Slot 1 999 code for Tool Items.
6. After the save has successfully been written back to your cart, take the cartridge out of the Powersaves and then place it back in.
7. Make a backup named something along the lines of 'Xorpad (X)' with X in this case being Pokemon X version so that you know which cartridge your keystream is for.
8. Copy your save back over from the desktop to the powersaves folder and restore it to get your original save back on your cartridge.
9. Download this tool: http://projectpokemon.org/forums/showthread.php?44175-Pokemon-Gen-VI-Save-Decrypter
Bin File Type Mac
10. Choose which game your using X/Y or OR/AS and then load up your Keystream which for this is named 'Xorpad (X)' that was created back in step 7 and select one of your saves for that cartridge. Hit Decrypt Save and then drag and drop the decrypted save onto PKHeX which can be found here: http://projectpokemon.org/forums/showthread.php?36986-PKHeX-(Gen-6-SAV-PKX-Editor)