Try disabling 3D sounds in your Options/Audio menu.
There could be several problems here.
1. If you are using custom music, be sure that you use the Sound Recorder application to convert it to an *.mp3, or leave it as a *.wav. if you don't , this can cause an error when entering a system using that music.
2. Do you have any custom factions? Factions can cause weird and unpredictable crashes when there is an error in their coding. I am actually having that problem right now as I type this.
3. This is a given, but is the jump gate set to go to and from to the correct systems? I know that New York is Li01. I don't know what your system is called.
4. Have you checked FlSpew.txt? That file can show most, but not all, errors in the game. A quick look at it can give you a relatively decent idea of what is causing the problem. If you have FlSpit.vbs, that is an even better way to check for errors because it filters out any irrelevant messages. You may have to modify its code, though, to reflect the location of FlSpew.txt.
make sure you havent installed the SDK over your FL install, as this can cause problems 
Oh, I thought the sdk (1.3 + 1.5) were just to make modding simpler and of course added the official 1.1 updates and fixed alot of ini errors that the original patch didn't address.
Must Not modify New York system, this is the base system in the game, that is it of course, if you use only FlEx.
NY system is max out already so if you want to add zone or jumpgate or jumphole you need to erase existing one.
So the best solution is to change the starting point of the player so you can avoid modifying existing system.