The problem is the 1.1.1a zip files really contain version 1.1.1.
The pasted text below shows what happens when you download 1.1.1a vs. 1.1.1 - you end up with the same files with the same checksums.
[aaron@core2] ~/jogl$ wget http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1a/jogl-1.1.1a-linux-amd64.zip
--2009-07-15 20:56:45-- http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1a/jogl-1.1.1a-linux-amd64.zip
Resolving download.java.net... 72.5.124.114
Connecting to download.java.net|72.5.124.114|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1311547 (1.2M) [application/zip]
Saving to: `jogl-1.1.1a-linux-amd64.zip'
100%[=========================================================================================================================>] 1,311,547 385K/s in 3.3s
2009-07-15 20:56:48 (385 KB/s) - `jogl-1.1.1a-linux-amd64.zip' saved [1311547/1311547]
[aaron@core2] ~/jogl$ unzip jogl-1.1.1a-linux-amd64.zip
Archive: jogl-1.1.1a-linux-amd64.zip
creating: jogl-1.1.1-linux-amd64/
creating: jogl-1.1.1-linux-amd64/lib/
inflating: jogl-1.1.1-linux-amd64/CHANGELOG.txt
inflating: jogl-1.1.1-linux-amd64/COPYRIGHT.txt
inflating: jogl-1.1.1-linux-amd64/LICENSE-JOGL-1.1.1.txt
inflating: jogl-1.1.1-linux-amd64/README.txt
inflating: jogl-1.1.1-linux-amd64/Userguide.html
inflating: jogl-1.1.1-linux-amd64/lib/gluegen-rt.jar
inflating: jogl-1.1.1-linux-amd64/lib/jogl.jar
inflating: jogl-1.1.1-linux-amd64/lib/libgluegen-rt.so
inflating: jogl-1.1.1-linux-amd64/lib/libjogl.so
inflating: jogl-1.1.1-linux-amd64/lib/libjogl_awt.so
inflating: jogl-1.1.1-linux-amd64/lib/libjogl_cg.so
[aaron@core2] ~/jogl$ md5sum jogl-1.1.1-linux-amd64/lib/*
44d5d11cfc275d4a78f8164004dbd717 jogl-1.1.1-linux-amd64/lib/gluegen-rt.jar
d086484bb61e4c8d1e0e8c29bbd873f8 jogl-1.1.1-linux-amd64/lib/jogl.jar
d56d73e9ca8fca87cb5084c7e68d6651 jogl-1.1.1-linux-amd64/lib/libgluegen-rt.so
f7aae1e9c98d0bd26d24580b8be63924 jogl-1.1.1-linux-amd64/lib/libjogl_awt.so
63db00d144295eeb85a0afded93183ce jogl-1.1.1-linux-amd64/lib/libjogl_cg.so
d3a649ef2c2d516eb34f2f6a8a258d8a jogl-1.1.1-linux-amd64/lib/libjogl.so
[aaron@core2] ~/jogl$ wget http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1/jogl-1.1.1-linux-amd64.zip
--2009-07-15 20:57:10-- http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1/jogl-1.1.1-linux-amd64.zip
Resolving download.java.net... 72.5.124.114
Connecting to download.java.net|72.5.124.114|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1311547 (1.2M) [application/zip]
Saving to: `jogl-1.1.1-linux-amd64.zip'
100%[=========================================================================================================================>] 1,311,547 264K/s in 4.6s
2009-07-15 20:57:14 (281 KB/s) - `jogl-1.1.1-linux-amd64.zip' saved [1311547/1311547]
[aaron@core2] ~/jogl$ unzip jogl-1.1.1-linux-amd64.zip
Archive: jogl-1.1.1-linux-amd64.zip
creating: jogl-1.1.1-linux-amd64/
creating: jogl-1.1.1-linux-amd64/lib/
inflating: jogl-1.1.1-linux-amd64/CHANGELOG.txt
inflating: jogl-1.1.1-linux-amd64/COPYRIGHT.txt
inflating: jogl-1.1.1-linux-amd64/LICENSE-JOGL-1.1.1.txt
inflating: jogl-1.1.1-linux-amd64/README.txt
inflating: jogl-1.1.1-linux-amd64/Userguide.html
inflating: jogl-1.1.1-linux-amd64/lib/gluegen-rt.jar
inflating: jogl-1.1.1-linux-amd64/lib/jogl.jar
inflating: jogl-1.1.1-linux-amd64/lib/libgluegen-rt.so
inflating: jogl-1.1.1-linux-amd64/lib/libjogl.so
inflating: jogl-1.1.1-linux-amd64/lib/libjogl_awt.so
inflating: jogl-1.1.1-linux-amd64/lib/libjogl_cg.so
[aaron@core2] ~/jogl$ md5sum jogl-1.1.1-linux-amd64/lib/*
44d5d11cfc275d4a78f8164004dbd717 jogl-1.1.1-linux-amd64/lib/gluegen-rt.jar
d086484bb61e4c8d1e0e8c29bbd873f8 jogl-1.1.1-linux-amd64/lib/jogl.jar
d56d73e9ca8fca87cb5084c7e68d6651 jogl-1.1.1-linux-amd64/lib/libgluegen-rt.so
f7aae1e9c98d0bd26d24580b8be63924 jogl-1.1.1-linux-amd64/lib/libjogl_awt.so
63db00d144295eeb85a0afded93183ce jogl-1.1.1-linux-amd64/lib/libjogl_cg.so
d3a649ef2c2d516eb34f2f6a8a258d8a jogl-1.1.1-linux-amd64/lib/libjogl.so