I own the D1 rather than the D1x, but here are a couple of possibilities for you:
1) Set custom function 27 (display mode) to 'Highlights' or 'Both'. When you preview an image it'll flash any hotspots black then white so you can easily see them and re-shoot if necessary.
2) Keep the exposure compensation set to -0.3 or -0.6 in situations where you know the highlights are likely to burn out: You'll have to brighten your images slightly in Photoshop (or a similar application), but that's better than losing detail.
3) Use RAW mode and process the images in Nikon Capture / QImage / Bibble. RAW mode gives you access to the full 12-bit dynamic range of the CCD rather than the 8-bit range of a JPEG and if you use the software to produce a 16-bit TIFF you'll usually find that bright areas of the image haven't burned out. You can then use Photoshop (or whatever) to save the image as a JPEG that keeps that detail.
Exposure accuracy with the SB-28DX was all over the place with the D1 when using the TTL modes, but I thought this was meant to have been solved with the D1x. The way to fix this on the D1 is to put the flash into A mode so it uses its built-in sensor. You might like to give that a try.