This issue occurs when the Bentley Transmittal app pool user does not have enough rights to configure RSA token to continue installation and/or security access to directories.
There two possible ways to resolve the situation.
1 .If you already have tried to deploy once and Bentley Transmittal app pool is already created, change this app pool's identity(in advanced settings) to local admin domain account.
Afterwards in BTS install directory(C:\Program Files\Bentley\Transmittals\wizard\server) edit TransmittalServicesWizard.xml
Please make backup before you edit, then remove this entry:
<appPools>
<appPool name="Bentley Transmittal App Pool" managedPipelineMode="Integrated" managedRuntimeVersion="v4.0" enable32BitAppOnWin64="true" processModelIdentityType="ApplicationPoolIdentity" addAsUserToDb="True" loadUserProfile="True">
<grantAccess directory="%ALLUSERSPROFILE%\Bentley\Licensing" />
</appPool>
</appPools>
Save restart the wizard and the installation should complete.
2. Running this command might help without the edit needed:
cd C:\WINDOWS\Microsoft.NET\Framework\v4.0.30319 aspnet_regiis.exe -pa "IIS APPPOOL\Bentley Transmittal App Pool" -full