OK, so this seams to be a bug when creating a preset using the new button on the preset manager and removing toolbar buttons.
I am going to create a support ticket so we can look into this in more depth.
In the mean time, to work around the problem, crate your presets when applying the HTMLEditor instance.
Go to Insert -> WebAssist -> HTMLEditor
Click the customize button next to preset and modify the toolbar buttons. When you click OK you will be prompted to save a preset.
In my testing, presets created this way did not have the same problem when applying the preset to another page.