There are several reasons why you might not see a radio ID on a transmission.
The biggest issue is with analog users on Motorola Type II systems. Radio IDs are not carried over the voice channel on those systems, so once you leave the control channel to follow the voice message, you won't get any further IDs. That is why programs like Unitrunker appear to work better on that type of system - they don't ever leave the control channel. You get the first RID in a conversation from the info sent over the CC, and then, if the conversation is carried on quickly enough that you stay on the voice channel for the whole conversation (never going back to the CC), you will not get another RID.
P25 systems, unlike Mot II systems, carry the RID on the digital voice "data packet", so you will see the RID when a digital user is speaking. This also applies to digital users on a Mot II system.
I don't have any EDACS systems in my neighborhood so I can't rightly say if LIDs (logical ID, the EDACS term for a RID) are carried over the voice path.
The other issue is what someone mentioned above - coming into a conversation after it has started. This is called "late entry" and you may not get the RID (at least for the duration of the current person speaking in the conversation) showing up in this case, for the same reason - you may have gotten to the conversation too late to see the RID when it was mentioned either on the control channel or in the voice data, if the voice data supports it.
As mentioned above, the "sorting" of RIDs (or TGs, for that matter) has no bearing on the success or failure of looking up either piece of data. In a trunking environment, the TG and RID are directly provided by the control channel (or, again, voice data) and can be looked up directly, unlike an analog signal, where you only know it is, for example, 413.8375, and have to listen for a bit to determine what its squelch code (if any) is, etc.