Hmm... interesting. Take my above post as suggestion, I've never seen the message you posted.
If you changed only the lights...
Do you still have the two versions? If you want, you can take a look on them in a special way. Compile each (this requires that you give them different names) with BSP only. I hope you use GtkRadiant unless this has no sense. So, after BSP-ing (without VIS and LIGHT) you can use the portal viewer plugin to see if there is a portal at the given coordinates in your problematic version, and you can take a look at the normal version to see the difference.