I came accross with the same problem:
- ubuntu, java 1.5.0_22, ant 1.8.2
- suse, java 1.5.0_08, ant 1.9.0
(yes not the identical environments but.. in 1.8.x it was working..)

Manifest is genereated in jar taks.

there were following differences:
- Manifest: only content of Ant-Version: , and Created-By:  (that could not
make problem)
- differences of jar files length,  jar from 1.8  has 6.2kB, jar from 1.9
has 6.3kB,  --> i thing this shows to different compressing.
and if I compare displayed content with kdiff3, it is different in some
parts.

As I have read in discussion thred something changed in zip algorithm. 
Question is, if there is a way to create "old style" compressed jar.

Regards
Vaclav





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