When JabRef writes jabref-meta data in @comment{} entries, it uses a fixed line with. Other programs that read and write the BibTeX file might not care about newlines in comments. An example of this is biber, wich I try to use as a BibTeX pretty-printer. Minimum working example:

Consider the following BibTeX file written by JabRef:

% This file was created with JabRef 2.11b4.
% Encoding: UTF8


@Misc{Paranoid2015,
  title           = {Don't Talk to Me About Life},
  author          = {Marvin the Paranoid Android},
  date            = {2015-10-21},
  date-modified   = {2015-10-21}
}

@comment{jabref-meta: groupsversion:3;}

@comment{jabref-meta: groupstree:
0 AllEntriesGroup:;
1 ExplicitGroup:Statically group entries by manual assignment\;0\;Para
noid2015\;;
}

Note the newline in the middle of a BibTeX key. When processing this file with the current development version of biber (previous versions removed comments altogether), it comes out like this:

@MISC{Paranoid2015,
  AUTHOR        = {Marvin the Paranoid Android},
  DATE          = {2015-10-21},
  DATE-MODIFIED = {2015-10-21},
  TITLE         = {Don't Talk to Me About Life},
}

@COMMENT{jabref-meta: groupsversion:3;}
@COMMENT{jabref-meta: groupstree: 0 AllEntriesGroup:; 1 ExplicitGroup:Statically group entries by manual assignment\;0\;Para noid2015\;;}

Note that the newline in the BibTeX key is converted to a space (Para noid2015), which breaks the groups tree.

Now, this could be considered a bug in either biber or JabRef. I tend to blame JabRef, since I can't see any reason why JabRef should write fixed-with @comment entries and thus rely on truly verbatim treatment of @comment entries.