Velveth flag question

[winsettz]

I've been generating

velveth Assem1 85 -create_binary -shortPaired -fastq -separate

upon closer examination of the manual, it should be

velveth Assem2 85 -create_binary -fastq -shortPaired -separate

Amusingly, the results are different

Final graph has 4275 nodes and n50 of 11961, max 59442, total 4748899, using 12959473/18913301 reads

Final graph has 4229 nodes and n50 of 11829, max 57667, total 4724268, using 13243576/18913301 reads

Obviously I need to directly compare contigs and see what the real changes were from an assembly standpoint...but I wonder how velvet is interpreting the results for the first velveth input if it is isn't the same as the canonical, second version.

Reposting to the velveth mailing list.