Joanne, It looks like you have spotted a bug in FSDirectory. However I am not sure if it is what is causing the problems you are seeing. I just checked a fix for this into CVS. Please try this newe version and tell me how things go.
One thing that might be confusing you is the file names in your index. A few facts: First, there is only ever one version of 'segments' and 'deleteable'. These are global files, not per-index. Second, segment names are integers in base 36 prefixed by an underscore, and are created in order. So segment _i precedes segment _k. Third, it is possible on Win32 to have incomplete segments remain for old segments. On Win32 an open file cannot be deleted, so Lucene keeps the list of names of files that it would like to delete in the 'deleteable' file. Doug