Take a look at the 'todir' property in http://ant.apache.org/manual/Tasks/checksum.html . This would imply that the first use will add files to the directory so that this will then change the checksum for the second use. A quick test shows this to be the case. Maybe you should specify a different directory to place the checksums.
Retired horse trader.
Note: double-underline links may be advertisements automatically added by this site and are probably not endorsed by me.