You need to check your model number to see if your PS3 is compatible with the E3 flasher. Yes it can be done on all softwares. If you don't install the clip properly your gonna keep getting errors and invalid dumps so its important to have a good connection with your clip to increase your chances of valid dumps. This also makes it much faster for you.
Look here how I have mine setup: unfortunately my e3 flasher doesn't want to work. But the way I setup should give a really good connection.
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