So the problem was that I assumed that if you don't define a location for the file then it would default to just the file in the root of the workspace - which I think is not unreasonable (in fact I didn't notice the location field). And if you do so you get the kind of unhelpful message below:

I created a new job that accepts a file parameter. I ran this job and selected a file. And I get this as the job output:

...
Copying file to
FATAL: d:\hudsonwork\workspace\generate_wer_submission_file (Access is denied)
java.io.FileNotFoundException: d:\hudsonwork\workspace\generate_wer_submission_file (Access is denied)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(Unknown Source)
at java.io.FileOutputStream.<init>(Unknown Source)
at hudson.FilePath$25.call(FilePath.java:1298)
at hudson.FilePath$25.call(FilePath.java:1294)
at hudson.remoting.UserRequest.perform(UserRequest.java:118)
at hudson.remoting.UserRequest.perform(UserRequest.java:48)
at hudson.remoting.Request$2.run(Request.java:287)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at hudson.remoting.Engine$1$1.run(Engine.java:60)
at java.lang.Thread.run(Unknown Source)

So it seems that Jenkins can't write the uploaded file to the directory. Which itself created.

I checked on the slave and the directory does exist, the path is correct and (as a different part of the job) svn files were checked out there.