CoreFTP
This is the package for CoreFTP Pro. On the download page http://www.coreftp.com/download.html there is an MSI package setup.msi.
I have already registered with CoreFTP for a site license and they sent me an RGF file. If you do a normal install and then import your RGF file you can export the .REG from HKLM\Software\FTPWare. This will allow you to merge the license onto your computers.
I think if you are using the Lite (Free) version then you can get rid of the 'REGEDIT -S' install line. You users will then get the nag screen.
<package
id="coreftp"
name="coreFTP"
revision="211612"
reboot="false"
priority="1">
<check type="logical" condition="and">
<check type="uninstall" condition="exists" path="CoreFTP" />
<check type="file" condition="versionequalto" path="%programfiles%\coreftp\coreftp.exe" value="2.1.0.0" />
</check>
<install cmd='msiexec /i %SOFTWARE%\coreftp\setupp.msi /qn ' />
<install cmd='cmd /c REGEDIT -S %SOFTWARE%\coreftp\coreftp.reg ' />
<remove cmd='MsiExec.exe /x{1603C07E-4F28-4B7D-A193-EA04E92C2355} /qn ' />
</package>