I can't speak to the XLights conversion issue, but this is a known LOR controller "feature" - a LOR channel will stay at the intensity the last command it received set it at. The software generally doesn't send out "keep it at intensity xxx" like DMX does.
The beginning of your LOR sequence sets the intensity of that channel at 100% once, and then forgets about it. Apparently the XLights conversion is ignoring that first setting if at 100%. Setting it at 99% apparently gets around that.
I have a "Tune To" sign on a channel, that I originally set to 100% in a background sequence. Since I do at times copy sequences from other people, I found I had accidentally pasted to that channel. The "Tune To" sign would go out/be dimmed/something until the background sequence would start over, then go back to 100% until the next time something in a foreground sequence changed it again.
That's a little more extensive than what you're experiencing, but the hardware reason is the same.
Keeping that in mind, you may want to vary the intensity by a percent or two several times during your sequence, just to make sure that channel sees a change and reacts to it. I do that now, even though I'm not using the XLights for other than test purposes.