I think the logic goes something like this: first ever effect command on a track affects all the time before it, so when it jumps back to start; 1001 is the one affecting if it is the first ever command on that track.
For me this is useful if I for example add a reverb effect on a track more near the end of a song, and I want the reverb to be off before that point. So where I add reverb to be on, I add one pattern or some lines before that a off command, to make the reverb to be off in the beginning of the song.
Solution is to put desired on/off commands on the first line of pattern where u are jumping to. Or dont put commands in the tracks at all so switchin effects on/off wont change when jumping in time (this concerns more live playing situations)
hmmm, Now I understand that especially when looping live this is not always what you want, if u forgot to set commands on the first lines, or not at all.
Maybe U can share example .xrns file here to look at. So we can be sure ; D