Sorry that it took so long to reply but I really wanted provide you with a concrete example. Unfortunately it seems inconsistent.
The entries I'm talking about are "INFO download taskname Downloading: file"
To be fair it all started when logrotate changed namingconvention from .1 .2 etc to dates.
I used to have a script running alongside that read the log, colored it, categorized entries for easier interpretation etc and spit that out to screen but I have disabled that while testing.
One thought though, could it be that if the file flexget.log is removed that the first entry is not properly logged?