Gradle jar size different from jar command

Q: Well, you say the two jar files are of different sizes, but you only told us the size of one of them.
A: The bad jar is 12,939 bytes. The good jar is 13,091 bytes. I create the good jar by manually updating its MANIFEST.MF file with this command:

jar uvfm my.jar META-INF/MANIFEST.MF

This command does not change the contents of the MANIFEST.MF file. All the diff tools so far show the contents and size of the MANIFEST.MF file to be the same (albeit with different timestamps). Why does this command change the size of the jar then?

Q:You also compared the file listing and you say the only difference was the timestamp on one of the elements. You’re saying that otherwise the jar files were identical?
A: I used your suggested commands and posted the results to show that the only difference was the timestamp. I also ran pkgdiff on the jars and it reported their contents were unchanged from one jar to the other.

In reviewing your suggestions I see that I ommitted the “-c” in the diff command. Here is the full output:

diff -c bad.lst good.lst
*** bad.lst	2015-06-19 08:13:45.000000000 -0500
--- good.lst	2015-06-19 08:13:37.000000000 -0500
***************
*** 2,8 ****
       0 Wed Jun 17 16:17:30 CDT 2015 net/
       0 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/
       0 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/
!     68 Wed Jun 17 16:17:30 CDT 2015 META-INF/MANIFEST.MF
    3533 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/RCSRequest$_getResponse_closure1.class
    5527 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/Constants.class
    6905 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/RCSResponse.class
--- 2,8 ----
       0 Wed Jun 17 16:17:30 CDT 2015 net/
       0 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/
       0 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/
!     68 Wed Jun 17 16:21:40 CDT 2015 META-INF/MANIFEST.MF
    3533 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/RCSRequest$_getResponse_closure1.class
    5527 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/Constants.class
    6905 Wed Jun 17 16:17:30 CDT 2015 net/rcsdev/http/RCSResponse.class

Additional Information
Jar built using Gradle 2.4, --version output looks like this:

$ gradle --version

Gradle 2.4

Build time: 2015-05-05 08:09:24 UTC
Build number: none
Revision: 5c9c3bc20ca1c281ac7972643f1e2d190f2c943c

Groovy: 2.3.10
Ant: Apache Ant™ version 1.9.4 compiled on April 29 2014
JVM: 1.8.0_31 (Oracle Corporation 25.31-b07)
OS: Mac OS X 10.10.3 x86_64

The exception thrown by the application looks like this:

intradoc.io.zip.IdcZipException:
!syZipFormatNonZeroDirectoryLength,org/
at intradoc.io.zip.IdcZipFileFormatter.validateCentralDirectoryEntry(IdcZipFileFormatter.java:453)
at intradoc.io.zip.IdcZipFile.init(IdcZipFile.java:195)
at intradoc.loader.IdcLoaderElementList.makePathElement(IdcLoaderElementList.java:221)
at intradoc.loader.IdcLoaderElementList.addPathElement(IdcLoaderElementList.java:361)
at intradoc.loader.IdcClassLoader.addClassPathElement(IdcClassLoader.java:406)
at intradoc.server.ComponentLoader.loadEnabledComponent(ComponentLoader.java:771)