Well the first thing I see is you are using an old version of URTC.COM with -tp argument - this had an option for the Superbrain (-ts) but I later separated them into two COM files. The earlier version also had a few bugs in its date derivation code. So if I were you I'd try the later version first. Oddly I didn't update the version number - still says v0.2 but the help message is different.
Second thing I see is a missing space in the uIDE XDRIVER signon prompt. I would not have released it like that (I'm a bit of a stickler for prettyness).
So I am wondering if your drive has got corrupted. uRTC is a dead simple design and there is very little that can go wrong. In fact, it is so simple that I didn't even bother prototyping it before sending it for board production.
Looking at your SURVEY.COM output, I see C0-C7 missing. uRTC uses C0-CF (thanks to Epson's chip interface) and so all of these should be listed as active. You've only got C8-CF showing and this suggests a problem with the connections to the clock chip. If you have a multimeter, please check the following connections for continuity:-
Clock chip pin 4 to CPU A0
Clock chip pin 5 to CPU A1
Clock chip pin 6 to CPU A2
Clock chip pin 7 to CPU A3
Or, if you have a logic probe, see if the clock chip pins are active by probing them for activity. If they are flashing then you know they are connected to the CPU.
Next, test the 668 in the same way. Pins 2, 4, 6 and 8 are A7-A4 respectively.
If those are OK, put the probe on the /CS0 pin of the clock chip (pin 2) and try to run uRTC (no arguments needed). If there is activity then you know the 668 is working and selecting the clock chip.
If all else fails you'll need a new clock chip. I do not know if they are known for fragility. If you want to send me one or more chips to try in one of my units, PM me.