I believe to have found the issue. By default, Eclipse seems to construct the jar differently, leaving out entries for directories.
Investigating the archives with unzip -v reveals some interesting details.
File from building with Ant:
Archive: JSGFDemo.jar
Length Method Size Cmpr Date Time CRC-32 Name
-------- ------ ------- ---- ---------- ----- -------- ----
0 Stored 0 0% 2013-03-31 03:13 00000000 META-INF/
284 Defl:N 210 26% 2013-03-31 03:13 ddd976ff META-INF/MANIFEST.MF
0 Stored 0 0% 2013-03-31 03:08 00000000 edu/
0 Stored 0 0% 2013-03-31 03:08 00000000 edu/cmu/
0 Stored 0 0% 2013-03-31 03:13 00000000 edu/cmu/sphinx/
0 Stored 0 0% 2013-03-31 03:12 00000000 edu/cmu/sphinx/demo/
0 Stored 0 0% 2013-03-31 03:13 00000000 edu/cmu/sphinx/demo/jsapi/
0 Stored 0 0% 2013-03-31 03:13 00000000 edu/cmu/sphinx/demo/jsapi/jsgf/
7391 Defl:N 3501 53% 2013-03-31 03:13 938438dd edu/cmu/sphinx/demo/jsapi/jsgf/JSGFDemo.class
798 Defl:N 326 59% 2013-03-31 03:13 647722fc edu/cmu/sphinx/demo/jsapi/jsgf/books.gram
204 Defl:N 140 31% 2013-03-31 03:13 789bb514 edu/cmu/sphinx/demo/jsapi/jsgf/commands.gram
9295 Defl:N 1500 84% 2013-03-31 03:13 3b519044 edu/cmu/sphinx/demo/jsapi/jsgf/jsgf.config.xml
1589 Defl:N 473 70% 2013-03-31 03:13 60075af0 edu/cmu/sphinx/demo/jsapi/jsgf/movies.gram
299 Defl:N 195 35% 2013-03-31 03:13 42e94d32 edu/cmu/sphinx/demo/jsapi/jsgf/music.gram
666 Defl:N 288 57% 2013-03-31 03:13 ca4b72f9 edu/cmu/sphinx/demo/jsapi/jsgf/news.gram
-------- ------- --- -------
20526 6633 68% 15 files
Jar exported using eclipse:
Archive: JSGFDemo-eclipse.jar
Length Method Size Cmpr Date Time CRC-32 Name
-------- ------ ------- ---- ---------- ----- -------- ----
180 Defl:N 134 26% 2013-03-31 23:35 1e681d3b META-INF/MANIFEST.MF
7338 Defl:N 3537 52% 2013-03-31 23:29 ed8c4c3f edu/cmu/sphinx/demo/jsapi/jsgf/JSGFDemo.class
798 Defl:N 326 59% 2013-03-31 13:21 647722fc edu/cmu/sphinx/demo/jsapi/jsgf/books.gram
204 Defl:N 140 31% 2013-03-31 13:21 789bb514 edu/cmu/sphinx/demo/jsapi/jsgf/commands.gram
9295 Defl:N 1500 84% 2013-03-31 13:21 3b519044 edu/cmu/sphinx/demo/jsapi/jsgf/jsgf.config.xml
1589 Defl:N 473 70% 2013-03-31 13:21 60075af0 edu/cmu/sphinx/demo/jsapi/jsgf/movies.gram
299 Defl:N 195 35% 2013-03-31 13:21 42e94d32 edu/cmu/sphinx/demo/jsapi/jsgf/music.gram
666 Defl:N 288 57% 2013-03-31 13:21 ca4b72f9 edu/cmu/sphinx/demo/jsapi/jsgf/news.gram
-------- ------- --- -------
20369 6593 68% 8 files
After a quick google, I found the "Add directory entries" option in Eclipse's jar export wizard.