I have not heard of the 990 having a problem with 96kHz sources as a general rule, but I've also never fed a 96khz digital signal to the 990 nor can I find explicit mention of support for it in the 990's manual.

A couple of issues: DVD-Audio cannot be output via coaxial in its true multichannel form (aside from the bandwidth requirements of MLP, the copy protection forbids it) so you are being limited to a two-channel downmix of the original lossless 5.1 signal when playing the DVD-A format (a format which, by the way, is for all intents and purposes dead and buried - speaking as someone with a section of my CD library devoted to them and to SACD). To hear DVD-Audio in its proper form, you need to be using a 5.1 analog output. Also, not all DVD-Audio discs will include a DTS track. As DTS is a lossy format, it is not as good a choice as the DVD-A track.