As long as the portable applications are not inside a Zip, Rar, etc. archive, CryptoPrevent will not cause an issue, even on with all the options ticked.
When a malicious executable is run, the first thing it tries doing is hiding itself somewhere. In the past, this was easily done - Just copy itself to the Windows or System32 directory. However, with the UAC feature of Vista onwards and most business employees not having admin access anyway, an infection has only a few places to hide. So what most Malware does now is it tries placing itself in a hidden directory where a non-Admin account can write to, usually the Appdata, Temp or Recycle Bin folders. Once a copy is made in a suitable location, the Malware then runs its copy, so even if the user deletes the original file after noticing it won't open or do anything, the Malware is still running from its hidden location. From my testing with Malware files in a virtual PC, some that came from fake DHL e-mails even throw up Notepad with random delivery details to give the impression that the user simply received a wrong delivery notice.
Unlike Malware, a legitimate portable application does not go about trying to run a hidden copy, so it simply runs from its existing location. So in theory, CryptoProtect shouldn't stop any legitimate portable applications from from running.
The main exception is if the portable application is still inside a Zip file, as Windows will extract the executable to the Temp directory before it tries running it. This will fail, as CryptoProtect prevents executables from running in the temp directory.