There are several options in the IDF Editor for the order of
objects. In the current version, they are listed in the "Save
Options" dialogue on the File Menu.
If you select the "sorted" option, I believe you will get all
the objects of the same class grouped together.
Originally, that was the only option. But some people like to group
things in hierarchical order (e.g.,
Zone
Surfaces
Internal heat gains
and the sorted object messed that up for them.
Hope this helps. I would encourage you to move up to the latest
release. (Our next release, V3.1, is targeted for early
April)