Which brings me to the other thing I neglected to mention (sorry, as it turns out I left out quite a lot of detail originally).
The automated system uses only Java libraries or plink.exe to connect...
Yep, under normal circumstances where users log in and do all sorts of funny stuff I'd agree with him. I probably should've elaborated in my original post a bit.
I'm stuck with a sysadmin telling me that the history files aren't sufficient to establish whether a certain account ran certain commands or not, which just...