The PLINK/SEQ website (http://atgu.mgh.harvard.edu/plinkseq/) and codebase has been substantially updated over the past few months.
Version 0.08 is now officially released. We strongly suggest upgrading to this version. There are a large number of additions, fixes and a few changes (in syntax, etc) -- some of these are described here: http://atgu.mgh.harvard.edu/plinkseq/changelog.shtml
Please note that projects and databases are not backwards compatible to versions prior to 0.08.
There almost certainly remain more than one or two rough edges, so feedback is appreciated.