With my working directory set to the install directory for the FTP sderver software, I issued this command to install a Windows service for the FTP server:
bin\service install LabKeyFTP -xml res\conf\ftpd.xml

Note that the instructions at the end of https://www.labkey.org/wiki/home/Documentation/page.view?name=configureFtp are missing some "\" characters in the command line.

This does install the service. However, when I attempt to start the service, the following error is logged:
[2008-02-19 10:37:55] [info] Running Service...
[2008-02-19 10:37:55] [info] Starting service...
[2008-02-19 10:37:55] [947 prunsrv.c] [error] Failed creating java
[2008-02-19 10:37:55] [1202 prunsrv.c] [error] ServiceStart returned 1
[2008-02-19 10:37:55] [info] Run service finished.
[2008-02-19 10:37:55] [info] Procrun finished.

I searched on the web for errors like this, and found some that said it was because JAVA_HOME wasn't defined and/or the java path wasn't in the system "Path" environment variable. I added a system-level JAVA_HOME environment variable, and added the same folder to the end of the system Path variable. I rebooted, but the service still returned the same error.

I found another note that said it couldn't deal with spaces in the path names, so I changed the paths to the short-name equivalent (C:\PROGRA~1\LABKEY~1\etc), rebooted and tried again, but it still failed with the same error.