Yeah,  I hear ya. Perhaps reinstall would fix a few things(?) (delete your links first (you have them in a file if you wish to reapply them)).
 
Perhaps this will help if you wish to try and clean it up ...
 
Think of it like this (simplified):
The synth Browser looks to the Programs which point to and load all the Elements (and FX/settings). The Elements, which can also be saved/loaded individually, look to MultiSamples for sounds.
 
This is how mine looks:
 
Core / Rapture Pro:
HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software:
ContentDir              %CakeHome%\Cakewalk Content
SampleDataDir           %SampleHome%\Cakewalk Sample Data
 
%ContentDir%\Rapture Pro
  \EG
  \Elements
  \MIDI
  \Programs              (.prog, etc)
  \Sample Pool
  \SG
 
%SampleDataDir%\Rapture Pro
  \LFO Waveforms
  \Mutisamples           (.sfz (multi), .wav (single), etc)
  \Tunings

If Samples can't be found, Rapture Pro also looks in the "Sample Pool" dir.
 
Additionally (which should have been scanned/copied during the installer ... but wasn't necessarily handled correctly til update 1):
HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software\Rapture Pro\2.0
Dim Multisamples Path         %CakeHome%\Dimension Pro
Rap Multisamples Path         %CakeHome%\Rapture
 
Legacy:

Dimension Pro (dp):
HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software\dp
contents folder               %CakeHome%\Dimension Pro
multisamples folder           %CakeHome%\Dimension Pro
 
Rapture (rp):
HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software\rp
Contents Folder               %CakeHome%\Rapture
 

Regarding Orchestral Stacks / Accented Trem Huge:
SFZs in:
%SampleDataDir%\Rapture Pro\Multisamples\Dimension Combo Textures
E1: Full Strings Tremolo Huge.sfz
WAVs in default_path=..\Garritan Pocket Orchestra\Section Strings\Full Strgs KS Combo Samples\
E2: Full Strgs Short Bows Huge Alt.sfz
WAVs in default_path=..\Garritan Pocket Orchestra\Section Strings\Full Strgs KS Combo Samples\
 

this stuff's coming across like a developer's joke :-S