No, it's not a problem. I do that all of the time. Are you sure that it saved? Are the tweaks still there?
Here's the longer and more helpful answer.....
After naming a preset, you have to click anywhere for the name to take. I usually hit 'Enter' on my keyboard (it seems quicker?). So sometimes when you hit the 'Save' button right after editing the scene or preset name, all that happens is the new name gets changed, but the 'Save' function didn't happen. You have to hit 'Save' again and verify that the 'Edited' light does out on the 'Save' button (and/or on the hardware).