I have a log file which is a large XML document comprised of various sub-documents that take a while to run. Each job writes its data to the file as the output is generated, but the whole XML document isn't closed (appropriate closing tags, etc) until the whole set of jobs is complete. Sometimes, the writing of the log will pause for more than 3 seconds (the default value of time_before_close), and so Splunk was consuming that file half-way through.
If you're seeing events broken before they're complete, consider MAX_EVENTS (it defaults to 256 additional lines, so if you have those multi-line events showing a linecount of 257, this could be the issue), or possibly TRUNCATE.
