I've dealt with a few of my own Nexus issues recently, maybe I can help...
First, you need to make sure your setting the nexus in the correct place. If you run the engine through WED, it will use the nexus which you set in the Map Properties in WED, but if your running the engine through SED, it will use the Nexus set in the Configuration panel in SED.

Publishing, I believe, causes the engine to use the Nexus set in WED, so make sure they are set correctly. The way I tested this it to have a panel with Digits showing the max_entities variable, which by default is equal to your Nexus * 10. When I ran the game, these digits showed up on my screen and I knew what level my nexus was set to. This is also when I noticed that it changed, depending on whether I ran the engine through SED or WED.

If you press F11 while running your game, it will call up the "Statistic Panel" which I've found to have very little supporting information in the manual. This panel will show a whole bunch of variables like the current fps and current nexus. Nexus is the first number in the Memory column, and this may help you determine what's wrong with your level.