I figured it out. My custom upload.html (sorry -- I forgot to mention that detail!) is based on the default from the general assay. My custom upload.html was supposed to have copied the behavior of the default of allowing multiple serial uploads without navigating way from or reloading the upload page. I realized today that the submission was always failing on the second serial submission without a page reload. Turns out I failed to reset all the properties of LABKEY.page.batch between submissions. Once I cleared all of those properties including lsid, it started working all the time.

-Will