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This is not preverifier problem. Preverifier does not touch original manifest file, it uses standard JDK "jar" utility to create resulting JAR.
For instance, you can unpack you JAR file and pack it again using following command (consider, that original JAR is unpacked to the folder "original):
jar -cfm <path to new JAR file> original/META-INF/MANIFEST.MF -C original
You can see that properties order in MANIFEST is changed.
So, you have 2 options here:
1. Open a bug/RFE against JDK
2. Do not use preverifier JAR mode: preverify unpacked classes without creating resulting JAR.