A couple things I noticed dealing with fields in the current version:
1. All selected fields reset when you go back in to the event to edit, even if you do not go to the fields tab. It is a nuisance to have to reselect all fields every time you edit an event.
2. If you are not using new lines for choices using a checkbox or radio buttons you must end the choices with a "|" to have a box or button show up. If you use new lines the end "|" can be left out.
3. Is there any way to add a custom email message for individual events?
As posted in the announcements thread, you very much need to update. The .12b release had issues with saving event fees and fields. Update to the current package and you'll find this as resolved.
Regarding the checkbox issue... never seen or heard of that before. You should not be using or need an ending |. Will check into that.
All events have the ability to enable and create a custom thanks email and custom admin notification email.