When you went through the cloning process with the software, when it told you to shutdown and set the bios boot sequence to the SSD, did you disconnect the old HDD for the first boot?
Typically, when I clone OS drives over to another drive, once that cloning is completed and you have to set the boot sequence in the bios, I recommend disconnecting the old drive physically before booting into the new drive for the first time. Just a peace of mind to ensure that it's not booting into the wrong drive.
It doesn't sound like the cloning worked properly the first time around. Perhaps you can format the ssd and retry?
Also, did you pay for that program? The 'free' part of that program only provides some preview features.