I've been trying to fix this pretty much ever since SO5 came out. Here's how you do it (on Windows):
1. Go to your StudioOne folder and right click the subfolder Presets.
2. Select Properties and click the Security Tab
3. Click Edit. In the name list select User(s) and check all the boxes you can. This should give you full control over this folder and everything in it, which means you can now save Presets again. If this doesn't work you can always try it for every subfolder under Presets.