Hmmm...I'll have to look into that. Meanwhile, three possibilities:
1) If it's a custom skin for a single portal, the easiest solution is to not use the Logo control and instead just embed the HTML for it directly.
2) Add a bit of Javascript to the skin for the splash page to set a cookie and redirect to the home page if the cookie is present.
3) Don't use a splash page and create the home page skin so it's like this:
<div id="SplashPage" style="display:none"> splash content </div>
<div id="HomePage" style="display:block> regular skin content </div>
You can then add some script to the page to check for a cookie and if the cookie is not present, toggle the "display" style attribute on both divs, but if it is present, do nothing.
If you need help with the JS code for #2 or #3 let me know and I'll post snippets.
Nik