Just tested to copy the westernq3 beta2.2 version of Train into the SG_1.0, and it does the same little freeze every 2 second. Of course Train works perfectly in wq3 beta2.2, so the map is not to blame. And just for fun, I have copied the SG_1.0 version of Train into my wq3 beta2.2, and it run fine. In fact this little annoyance appears on ALL map, except that the effect is magnified on Train (BTW Train use a lot of moving things, so is more vulnerable than other map).
I have tested Train on all version of the game I have.
It works well on : wq3 beta2.2, the last SA version still named WesternQ3, the first SA version named Smokin' Guns.
It works bad on : RC2, and SG_1.0
In addition, I have also tested to import SG like a mod in ioQ3, and good news, Train works well, those nasty little lag/freeze (that appear even in single player game) don't happened. So when the game will be backported to ioQ3, this bug will disappear.