Just going to quickly submit an update here despite the thread being closed:
For those waiting with bated breath, we figured out what went wrong here. Yes, there was an introduced bug, due to differences in the way the math was handled for the scaling/spawning system from BG1 to BG2. We attempted to make the BG1 maps use the BG2 system, but, when it came to this particular aspect we basically didn't go far enough.
Interestingly: in the course of investigation we found out that BG2 doesn't really use the random spawn system the same way that BG1 does. While it fits the style of gameplay in BG2 (sort of a more linear storyline), it's a kind of cool discovery in terms of giving us options for new content.
So: this fix should be present in our next patch. Thanks all involved for bringing it to our attention. Feel free to shoot me a message if you have questions.