First off, thanks for all the great advice that has led me to the D100, SB-28DX, 24-85 2.8-4, 80-200 2.8 and 85 1.8.
I have been noticing this underexposure using the SB-28DX myself and I have found a few of solutions.
Well for one thing, I always use a sto-fen flash diffuser http://www.stofen.com/ And I THINK that maybe DTTL Matrix uses preflash to set the exposure and this preflash doesn't go through the diffuser, therefore when the diffuser is on the exposure is off by -1. However if I press the mode button on my flash and change it from DTTL MATRIX to simply DTTL the results seem better. (Is anybody else who's having under exposure problems using a diffuser?)
I will go away and do some tests this weekend. But I wanted to share my experiences so far. Here are the 3 settings that seem to work better.