Hey Bob,
 
It sounds like you've changed some stuff during your installations. If you've got both:
 
D:\Cakewalk Content\Cakewalk Sample Data\Rapture Pro\Multisamples
and
D:\Cakewalk Content\Rapture Pro\Multisamples
 
That means at some point you likely changed the default Sample Data path during the Rapture Pro installer. You can either change this from the registry:
 
HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software\SampleDataDir
 
Or re-run the Rapture Pro installer and make sure it's pointing exactly where you want it. The default location is going to be C:\Cakewalk Content\Cakewalk Sample Data (it will automatically add Rapture Pro\Multisamples). If you've simply got all of your Cakewalk Content on another drive, it's best to just change the drive letter for simplicity. 
 
For now, I'd suggest you cut/copy/paste the contents of D:\Cakewalk Content\Rapture Pro\Multisamples to the folder in Cakewalk Sample Data (after being sure this is where Rapture Pro is actually reading).
 
 
The programs read based on where you have Cakewalk Content installed to. So in your case, if the value in your registry already exists for D:\Cakewalk Content, it will then automatically place the programs in Cakewalk Content\Rapture Pro\Programs.
 
Content (expansion pack/factory) installers, are going to install based on what the existing registry keys are. So if they detect Rapture Pro is installed, they'll go to your Cakewalk Content folder and into Rapture Pro's programs folder. The multisamples will go into either Cakewalk Sample Data, or your existing Rapture/Dimension Pro multisample folders depending on your install configuration. Rapture Pro will migrate your existing Rapture 1 programs/expansion packs by copying them to Cakewalk Content\Rapture Pro\Programs. 
 

YAY - it seems all is working properly now, and I also finally understand what the relationship is for the multi-samples and the Registry keys.
 
I sure do appreciate all the help, 
 
Bob Bone