The clock file included in the download is what forces the startbutton window to show on your screen when you log in, without it the window will still "hide".
The file you will need to edit to make the startbutton window show on login is called eq2ui_mainhud.xml. This tells the game that you are using a custom window when you boot up the game. As before - right click and choose edit on the file named eq2ui_mainhud and add the following line above the </Page> part:
Since you are already using a custom clock then you have two options; either replace your existing file with the one included, or edit your existing clock file with the following steps:
1) open your custom ui folder and find the file named eq2ui_clock.xml, right click that file and choose "edit"
3) Use the "find" ability in Notepad and type in: Name="Clock"
4) Once it locates that line add a space and then add this code:
The second line in this file should look very much like this once you finish (unless there are other things added in):
<Page allowcloseontop="false" eq2usescomwndcontrols="true" Location="524,96" Name="Clock" OnShow="show_window=(MainHUD.StartButton) show_window=(MainHUD.StartButton)" PackLocation="center,top" PackLocationProp="-116/0001,0096/0001" ScrollExtent="216,38" Size="216,38" UserMovable="true">
I will not be able to check back here for a week, so I won't be able to offer support for this until next friday (3rd). If you are still unable to get this to work or are unsure how to do the above, you're welcome to post a copy of the clock file you are using now and I can edit it for you and repost for you to copy/download.
EDIT - It just occurred to me - also make sure that you are copying the files out of the unzipped folder and not dropping the entire unzipped folder into your custom UI folder.