I had the same issue, but did a complete reinstall of my Runtimes this summer. Here's the process I followed.

1. Create a separate folder on your drive called "Runtimes"
2. Within this folder, create a series of folders according to category.  Some of mine were Accessories_Buildings, Accessories_Weapons_Modern, Clothing_Fantasy, and so forth.
3. Within each subfolder, create another folder called "Runtime". This allows Poser to recognize that this is a Runtime directory.
4. Add each separate Runtime Directory to your Runtimes list in Poser by using the "Add Runtime" command.
5. Now, that you've got the categories set up, go ahead and install all your content. I used 3D Content Installer, available here on Renderosity. It's well worth the ten bucks because it automates the installation of your runtimes. Set up the archives you want in one particular runtime, point it at the folder you want them installed into, and then go for coffee.

I was able to do a complete reinstall of 32 GB of content in about a day and a half, and it's made working with Poser a lot easier.

Posermocap - Motion Capture animations for Poser and Daz3D.