I am just wondering if you inserted the chapter points in the whole original project *before* you split it in two (at least that is what I am assuming was your general work flow)? If so, it could be that when you split it, the cut came between two chapter points which had recorded different data for the length of the chapter before or after... And that could possibly give such a message as well.
The two pass conversion should not have caused any problem -- depending on what the format of the video was. You have never told us that. If it was standard definition DVD-compatible mpeg-2, then that would not have caused any problem at all -- just improved the quality a little, which is what it is designed to do. If however, you were rendering high definition mpeg-2 or mpeg-4, we generally don't recommend using either SmartRender or two pass encode.
As for the length of the second project, it could be a problem depending on what your project properties are or what you set as the burn properties. If, for instance, you have set the properties of your original project to high quality settings, including a bitrate of 8000 kbps, then that confirms you would not have had any problem burning the first part to one single DVD. With 8000 kbps and either Dolby or mpeg layer 2 audio AND two pass encode, you would have been able to burn around 70 minutes of video to a single layer DVD.
But not 90 minutes which is the length of your second part. To do that, you would need to drop the bitrate to around 7000 or maybe even slightly less. But the quality still should be very good using that bitrate...
