Well an idea occured just as I was closing this window after my above post so I went into eq2map updater's folder and renamed it's config file with all the directory and option settings with a .old tagged to the end incase it wasn't the issue.
Thankfully it was.
Would have been very nice if I got more of an error, and still not sure why the config was causing a problem, but it was, and the only error was that flash of a box as I mentioned. Now it's working fine.