Nikon's flash technology fires pre-flashes in TTL modes. By the way, the D1's manual is incorrect, these pre-flashes are not canceled if you use a Speedlight in bounce mode on a digital camera (as is the case on film SLRs). So, you need to get the camera out of TTL mode in order to measure flash output with an external meter.
Here's a useful trick: if you're only using the on-camera flash as a trigger to remote slaves, set it to manual flash mode at 1/64 power and measure the remote flash exposure directly with a pre-pop trial. Why? Because 1/64 power is enough to trigger your slaves, doesn't really put out enough energy to distort the exposure, and it doesn't force the Speedlight to recycle between flashes (i.e., the flash can fire again immediately). You can comfortably shoot at 1/64 power at the highest continuous frame rate any Nikon DSLR is capable of (or an F5 or F6, for that matter). Plus 1/64 power typically isn't enough to make any real change to your subject lighting.
Just one thing to watch for: Nikon recommends that you give the flash a rest every 30 flashes or so, lest you overheat the flash tube. Of course, on some Nikon cameras shooting raw, you'll fill the buffer with images before you get to that limit, while on an F5 you'll be changing film at 36 images, giving the flash a needed breather; but on shooting JPEG on most modern Nikon DSLRs you can easily exceed the recommendation enough that you should probably stop before the buffer fills.