Thank you Adam, that was it. I am running 32 bit on 64 bit for compatibility.
My keys were written to: HKEY_LOCAL_MACHINESOFTWAREWow6432NodeMicrosoftCryptographyCalaisSmartCards instead of HKEY_LOCAL_MACHINESOFTWAREMicrosoftCryptographyCalaisSmartCards
For whatever it means (reg query ...):
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System
EnableLUA REG_DWORD 0x1
ConsentPromptBehaviorAdmin REG_DWORD 0x5
FilterAdministratorToken REG_DWORD 0x0
For reference I fixed with similar to this:
Local $sRegKey = "\SOFTWARE\Microsoft\Cryptography\Calais\SmartCards\SynchrotekID"
If @OSArch = "X64" Then
$sRegKey = "HKLM64" & $sRegKey
Else
$sRegKey = "HKLM" & $sRegKey
EndIf
RegWrite($sRegKey)
RegWrite($sRegKey, "80000001", "REG_SZ", $InstallDir & "\opensc-minidriver.dll")
RegWrite($sRegKey, "ATR", "REG_BINARY", Binary("0x3BF81800008031FE450073C8401000900091"))
RegWrite($sRegKey, "ATRMask", "REG_BINARY", Binary("0xffffffffffffffffffffffffffffffffffff"))
RegWrite($sRegKey, "Crypto Provider", "REG_SZ", "Microsoft Base Smart Card Crypto Provider")
RegWrite($sRegKey, "Smart Card Key Storage Provider", "REG_SZ" ,"Microsoft Smart Card Key Storage Provider")