According to the documentation on the Ultimarc website:
Running from the command line.
You can run WinIPAC IPD from a command line giving an "invisible" way to download a specific keycode configuration to the I-PAC board. Just enter "WinIPAC nnn.IPC" where the correct IPC file is specified. This is how the Launcher program and MAMEWAH drives WinIPAC.
I would guess if you had a batch file that ran the programming utility then ran WinCab, you could do what you want.