I just experienced the missing Rapture samples/multisamples issue. I am using the older version of Rapture and using SonarX2-PE, so this may not help you. Here was how I fixed my problem.
(1) I ran Sysinternals-Process-Monitor to watch what Rapture does
(2) Discovered that Rapture searches in 5-6 different PATH possibilities for the samples
(3) My impression is that CW added a bunch of possible "mis-installation paths"
(4) However no collections of PATHs will always work for everyone
(5) On my machine, I noticed that the PATH <C:\ProgramData\Cakewalk\Rapture\Sample Pool> was the last PATH before Rapture gave up and threw a "missing sample error"
(6) From my wasted-time spent RE-SAVING Rapture Programs by manually loading the missing samples into Elements, I discovered that most of the missing samples were actually existing in the <C:\Program Files\Cakewalk\Rapture\Multisamples\CompleetBankSynth-ToSFZ> Folder
(7) So I just copied the entire contents of <C:\Program Files\Cakewalk\Rapture\Multisamples\CompleetBankSynth-ToSFZ> into <C:\ProgramData\Cakewalk\Rapture\Sample Pool>; the cumulative sample size is fairly small of this entire collection
(8) BOOM, no more missing samples; at least I have not been able yet to find any
Maybe this will work for you or some tweaked version of it.