Some more information on this -- looking through the logs I didn't occur to me to expand the entries for the long latency queries, but when I did I found:
The process handling this request unexpectedly died. This is likely to cause a new process to be used for the next request to your application. (Error code 203) -- You received this message because you are subscribed to the Google Groups "Google App Engine for Java" group. To post to this group, send email to google-appengine-java@googlegroups.com. To unsubscribe from this group, send email to google-appengine-java+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/google-appengine-java?hl=en.
