JabRef version 3.3 on OSX 10.11.4
Steps to reproduce:
I would expect that the {}s be either universally preserved (preferred) or universally removed.
Please let me know if you would like to see my preferences; however, I cannot find anything that would provoke this behavior.

Can a developer please weigh in on whether this is expected behavior?
I can't reproduce the problem with the latest developer build available under http://builds.jabref.org/master/. On save "A Library Based on {ENDF/B-VII.0} Using the {CPXSD} Methodology gets written to the bib file and is correctly read if I open the file again.
Could you please check the latest build and make sure that you don't have any save actions activated (under File -> Database properties).
(Your last step 5 is expected behavior.)
@tobiasdiez Thanks for taking a look at this! Indeed, when I save the file with {CPXSD} in the title using 3.4dev, and re-open, the {}s have disappeared. I do not have any save actions enabled.
See attached minimum database.
Looking at it with a text editor, I see {CPXSD} but when I load it in 3.4dev, I see CPXSD as shown below.

Very strange, I cannot reproduce on my machine either using the latest master build. Maybe an issue with the preferences?
Could you post your settings? Options -> Preferences -> Export preferences
Please see attached, as exported from 3.4dev.
jkulesza_settings.prefs.zip
Can confirm this is a preferences issue.
The issue is "Store the following fields with braces around capital letters: "title"" This is somehow broken. If you remove this setting, the title field will be loaded correctly.
Excellent, thanks for the quick diagnostics, can confirm that fixed it.
Should I leave this issue open to track the broken preference behavior?
I am kind of in favor of deleting this function as it performs too much magic and does not work correctly. It is also somewhat replaced with save actions, as they can handle the escaping with brakets as well. @JabRef/developers what do you think?
Advantages
:+1: for removing this preference option.
@simonharrer Please note that there is a website FAQ entry on this that will need to be modified/removed.
Q: BibTeX converts uppercase characters to lowercase in my title field. I know this can be prevented by wrapping uppercase letters in braces, e.g. {T}he life cycle of {A}tlantic salmon, but this is too much work. Can JabRef help?
A: JabRef has a setting that will automatically wrap all capital letters for certain fields in { } - this will make sure they are preserved in the LaTeX output. Under Options -> Preferences -> File -> “Store the following fields with braces around capital letters”, make sure the title field is included. To do this for several fields, write e.g. title;abstract. This setting automatically adds braces when saving the bib file, but you won’t see the braces within JabRef.
@jkulesza: Thanks for following up on this. Since the preference option is gone, we should also remove the FAQ entry.
Removed.
Most helpful comment
:+1: for removing this preference option.