I have noticed this occur after long durations on my external testing server, but have yet to narrow down the cause.
I will try to look into some long term local server testing, if you can find a quick way to make this happen please let me know, I should be able to get it fixed.
I don't think it should be related to packets, as I haven't changed how I deal with those lately, but it chould be somehow related to that.
Thanks for the reply. I think the fastest way to reproduce the lag and "can't keep up!" messages is to get on a flying pokemon and fly in a straight line to generate as much world as possible. My server starts lagging sooner if multiple people are playing and moving around the map generating chunks.