Again, I've literally never seen this before, so it's not just a problem with the dialogue file or the mod. Something has to have changed.
Those empty messages have been around, at the very least, since TotA got released. I don't remember, if they also happened in DL or DA, but they require certain race and/or alignment-combinations to appear, which could explain why you haven't noticed them before. In any case, this is definitely due to bugs in the GC2_Conversations.xml. I've solved most of them in my mod, but I'm not sure, if I got all of them. Testing them is a pain.
Anyhow, part of the problem is what MarvinKosh said, but there is more to it. All entries of a Topic need to be ordered in a specific way: starting with the Terrans, going through the Drengin, Altarians, etc, and finally ending with the Generic (Custom Race) entry (just like how they are ordered in the RaceConfig.xml). If there is no entry for a race at all, then the Generic entry will be used. If there is only a limited amount of entries for a race (like Terrans-talk-to-Generic), then the Generic entry will be used for the rest. However, this isn't always the case, leading the game to display an empty message (because it can't find the necessary entry). I'm still not certain why this is, but the easiest way to fix it, is to add all the missing entries.
There is still a lot I don't know about the GC2_Conversations.xml. Everything I do know, I've learned through trial and error, because there is no documentation about it.