P25, DMR and NXDN are the general names that correspond to the most common digital voice protocols that you'll typically here in the usual scanner bands. There are plenty of others - Tetra, iDen, Opensky are a few examples - that have more specialized applications. And yes, to the trained ear, they all sound different.
P25 is by far the most common digital protocol used by public safety agencies, mostly because it's endorsed by government for interoperability purposes. Therefore, grant funding to agencies often applies exclusively to P25 equipment. P25 audio can be used on conventional radio systems as well as trunked radio systems, and the same P25 voice protocol is used for both Phase I and Phase II systems.
DMR probably has a higher market share for business use because it's the protocol endorsed by Motorola. It can be used on conventional systems (simplex and repeaters), linked repeaters, or with various flavors of trunked systems. Those include Capacity Plus, Connect Plus, Capacity Max (all Motorola brands) and TIII (a common standard).
NXDN is the other leading digital standard for radio in the US. And again, it can be used on conventional systems or trunked systems. NEXEDGE is the trunking flavor sold by Kenwood, and it has two flavors (4800 and 9600). Icom IDAS is another brand of the NXDN standard.
In South Carolina, there are several P25 trunked systems around, with Palmetto 800 being the biggest and statewide accessible. The SC PSA is another one that's almost statewide, and you'll see some Phase II activity on it.
There are DMR radio systems (conventional and trunked) all over the state, and it's probably difficult to find an area that you can't hear DMR signals. TRBOMAX, the Charleston Wireless linked system, Capital City TBRO, the SCANA system, the SC HEART amateur radio system and dozens of smaller private systems are all based on the DMR voice standard.
NXDN isn't as common in SC, but the Fleettalk system has sites pretty much all over the state.
The Uniden DMR and NXDN licenses enable the scanner to decode voice/audio of those particular protocols. That means that if you tune to a frequency using either of those voice protocols, regardless of trunked flavor being used (if any), you should be able to hear the audio with a scanner that has those licenses applied. However, trunk-tracking a trunked system that uses these voice protocols is a different matter. Some scanners may track most or all of these different flavors of trunking, others may not. And for many of these systems, the RadioReference database is incomplete. This is particularly true with respect to channel numbers, which is a requirement for Unidens to properly track some of these system types. This MIGHT be where you're running into trouble with your 996. That's why it's important to have folks with the skill and software that can decode and gather this information and submit it to the database. But it's painstaking task. Whistler scanners, which don't technically trunk-track DMR and NXDN-based trunked systems, have an advantage in that they don't require channel numbers to "scan" these systems. And you don't have to pay for additional licensing.
The RadioReference Wiki has quite a bit of documentation about digital radios standards that will provide much more detail that I can post in the forum.
Just to get you started:
wiki.radioreference.com
wiki.radioreference.com
wiki.radioreference.com