strange behavior of count table

I have tried to make a count table using the group and name files. However, the count.seqs command does not create a matrix as usual. So I generated one using PERL – but when I run a command with my count table – it claims that one of my sequences is in the file multiple times, but grep (in unix) only finds the sequence once.

Is there a version of mothur that I should use that is relatively bug free?

Our current version can be downloaded here, It sounds like you have a file format issue. If you send your input files to I can take a look?