The ID's for the links are not advancing they seem to be stuck around 50. This is messing up the links of course. Any idea's?

Check your linksid.txt file to see what it says. It should contain a number that is equal to the highest number already used for a link in links.db. If it doesn't, edit the file so that it does.

As to why it would do that to begin with; have you modified anything in add.cgi or admin_html.pl? If so, check whatever you modified to ensure that you have not someone messed up the code that increments that counter. If you haven't then make sure all your files in your admin/data directory are chmod 666.

I hope this helps.