Indeed that could well be (and is certainly not intended like that). I checked the code
and found that "execute on start run" and "execute on stop run" are called inside
cm_transition(). That means they are executed on the computer which calls cm_transition().
If you use mhttpd and start a run through the web interface, then mhttpd runs on your
server and "execute on start run" gets executed on your server. If you stop the run
by your frontend running on the client machine (like if a certain number of events 
is reached), then "execute on stop run" gets executed on your client.

An easy way around would not to use "/Equipment/Trigger/Common/Event limit" which
gets check by your frontend and therefore on the client computer, but use 
"/Logger/Channels/0/Settings/Event limit" which gets checked by the logger and
therefore executed on the server computer.

Getting a consistent behaviour (like always executing scripts on the server) would
require a major rework of the run transition framework with probably many undesired
side-effects, so lots of debugging work.

Stefan