Hm no.
Can you give some more details?
What version of PGP Command Line are you running?
You're running both instances at the same time?
Are you sending the output to specific file names, or are you relying on the suggested file name of the encrypted file?
Does the second output file have the data from the first run appear first in the file, second in the file, or is the data all mixed up?
If you run with "--debug --verbose", do you see any interesting output?
Thanks.