To hopefully help any others with this issue:
We also had this exact error running webgisdr on our 10.9.1 environment (failing on server). A manual ExportSite for server produced the same thing. We confirmed the account used had explicit, full-control permissions to all the necessary directories. We also ran every available patch and rebooted the server, to no avail.
Following this support article for a similar, but not exact error, led us to take a look at the jobs folder, which was full of a bunch of old, inactive jobs. I created a new, empty jobs folder, and the utility ran successfully.