I'm not seeing any problem with spotlights here -- as long as Native Lights is checked in Output > Export, then the plugin is translating them into the MXS at export time, and they are working fine with Multilight. I'm not sure why you would be reassigning their emitter materials in Studio though; could you expand on this? Does the multilight issue only show up when you use a SW > Studio > Render strategy, or are you also able to observe it rendering directly from the plugin?
SW > Studio > Render strategy is only when it happens - I will try and elaborate when I get a moment. I got it to work by creatinga a new emitter material for each sw spot light and assigning them to each sw spot light in studio. When I exported the original sw file, only the feature emitters seemed to work in the first render. The SW spot lights did not cast any light. I'll confirm whether I had native lights on.
On the question of crashing Studio, sure, feel free to send me the file. It may not be necessary though, depending on what is happening. If it is crashing Studio when you attempt to render, it may be due to multi-materials vs. instances, which are currently a problem in the renderer. So, in that case, it would crash if you tried to render a region or viewport within Studio; in this case, I wouldn't need a file, since the cause is known. However, if it crashes just opening the MXS, then that would be some other issue, and I would want to get a file so I can try to diagnose it.
It crashes when attempting a render. I eventually isolated a group of components that were causing the problem. I'll send it any way when the deadline has passed. Luckily it was just some internal amplifier stuff inside a product. Not really visible.