Well it seems to have remained stable on Flatfile.. so that eliminates some possibilites at least..
OK, next I recommend running the clock up on the flatfile to the same year the MySQL db is in and see if it is still stable for the flatfile. If not, then the shiplist/missions/gfs are possibly to blame. Then you have some serious shiplist QA and gf settings to take care of.
A server can be perfectly stable on a shiplist and set of gfs in one era but not another (or one game year and not the next for that matter), it is critical to test in all years that the server will run.
Even so, if it is unstable on the flatfile in the current year, then test the current year on an older build (still on the flatfile) as well to determine if it is the build that has issues. (Dave Ferrell's build 37 is a good baseline, or build 36.)
Follow?
P.S. Did you use mission matching setting other than the default? (i.e. CaptJeff's Storm Season 2 gfs? - whic everyone but me likes, I find them very unstable - nothing personal Jeff...) If so use default mission matching settings. There are better ways to achieve what people try to do with the gf settings which are poorly understood. (trial and error)