From your description it sounds like you are using the OMIM search that is available at NCBI (http://www.ncbi.nlm.nih.gov/omim). Back in 2011 OMIM moved to a separate web site (http://www.omim.org/) and the download on the NCBI FTP site was frozen (ftp://ftp.ncbi.nih.gov/repository/OMIM/). The OMIM web site is now the main point of access, with NCBI providing a search interface to support existing usage patterns with users being pushed over to the OMIM site to get the actual data.

The main OMIM web sites (e.g. http://www.omim.org/) provide a web services API (see http://www.omim.org/api) you could use to get the result data in a structured format from which the required information could be extracted. Note that many of the genetic diseases described in OMIM are not associated with a specific gene as yet, and thus will not have an HGNC gene symbol associated with them. For further assistance with using OMIM I suggest you contact the folks at OMIM (see http://www.omim.org/contact). I am sure they are very interested in any feedback that will improve the service they provide.