Ros version is 6.40.5, strongswan - 5.5.1.mikrotik ros version? strongswan version?
try to increase log verbosity on strongswan side (and then on mt side) and report back
I got it, unfortunately, no one client was disconnected when latency goes high again.It's not supposed to help only pinpoint where problem is. After you've made a change didn't you notice higher disconnect rate of one (or few) stations?
I tried enable this option(look at configuration on first message), it's also not helps. Also I enable adaptive-noise-immunity option.I'm assuming here this is an outdoor installation. Maybe there are some hidden node issues.
Try setting rts/cts on clients and cts to self on the mikrotik ap.