The time stamp message does not seem to be sent in the middle of things like the SYST:STAT? command results like some people have reported. It can come out while one is in the middle of sending a command to the unit... when that happens that command is corrupted and you get an "undefined header" response.
Also, it occasionally skips sending the time stamp message.
Odd. I have the exact opposite behaviour. I did think maybe you have a different firmware but your screen shot shows the same as mine, 1.0.0.2-01
Just to test my sanity I fired it up from cold and logged the results using PuTTY
=~=~=~=~=~=~=~=~=~=~=~= PuTTY log 2016.07.03 12:52:16 =~=~=~=~=~=~=~=~=~=~=~=
Symmetricom Boot Code ver. 1.01.01
Press Enter to go to boot
Image1: [1.0.0.2] [454535 bytes] [valid checksum:0x20AFA24] [timestamp:3]
Image2: [1.0.0.1] [454535 bytes] [valid checksum:0x2142B89] [timestamp:2]
Loading Image1
UCCM-P > *IDN?
Symmetricom,090-03861-03,W5609120082,1.0.0.2-01
Command Complete
UCCM-P > TOD EN
Command Complete
UCCM-P > c5 00 80 00 00 00 00 28 1c 52 00 00 20 60 c1 91 00 00 00 00 00 00 00 00 00 00 00 00 00 00 22 00 00 41 00 8f 50 00 00 00 00 97 72 ca
SYSc5 00 80 00 00 00 00 28 1c 52 00 00 20 60 c1 91 00 00 00 00 00 00 00 00 00 00 00 00 00 00 24 00 00 41 00 8f 50 00 00 00 00 9c 15 ca
T:STATc5 00 80 00 00 00 00 28 1c 52 00 00 20 60 c1 91 00 00 00 00 00 00 00 00 00 00 00 00 00 00 26 00 00 41 00 8f 50 00 00 00 00 6a d7 ca
?c5 00 80 00 00 00 00 28 1c 52 00 00 20 60 c1 91 00 00 00 00 00 00 00 00 00 00 00 00 00 00 28 00 00 41 00 8f 50 00 00 00 00 8a db ca
-------------------------------------------------------------------------------
090-03861-03 serial number W5609120082 firmware ver 1.0.0.2-01 LINK mode
-------------------------------------------------------------------------------
Reference Status __________________________ Reference Outputs _______________
Ref 8KHz 0: [LOS]
TFOM 9 FFOM 3
UCCM-P Status[OCXO WARMUP]
>> GPS: [no ref]
ACQUISITION .............................................. [ GPS 1PPS Invalid ]
Tracking: 0 ____ Not Tracking: 0 ________ Time ____________________________
GPS 00:00:43 [?] 06 JAN 1980
c5 00 80 00 00 00 00 28 1c 52 00 00 20 60 c1 91 00 00 00 00 00 00 00 00 00 00 00 00 00 00 2a 00 00 41 00 8f 50 00 00 00 00 7c 19 ca
GPS Invalid: not tracking
ANT DLY +0.000E+00
Position ________________________
MODE Survey: 0% complete
Suspended: track <4 sats
INIT LAT N 34:44:00.000
INIT LON E 135:21:00.000
INIT HGT +0.00 m (MSL)
ELEV MASK 5 deg
-------------------------------------------------------------------------------
Command Complete
UCCM-P > c5 00 80 00 00 00 00 28 1c 52 00 00 20 60 c1 91 00 00 00 00 00 00 00 00 00 00 00 00 00 00 2c 00 00 41 00 8f 50 00 00 00 00 77 7e ca
TODc5 00 80 00 00 00 00 28 1c 52 00 00 20 60 c1 91 00 00 00 00 00 00 00 00 00 00 00 00 00 00 2e 00 00 41 00 8f 50 00 00 00 00 81 bc ca
DI
Command Complete
UCCM-P >
After issuing TOD EN you can see I am typing in SYST:STAT? and it getting garbled amongst the timestamps, however this is just fine - no undefined header errors.
I also timed it so when I pressed enter I would get the TOD message in the normal output of SYST:STAT? which can clearly be seen. I then turned off timestamps with the TOD DI command and it was interrupted but the command completed with no undefined header errors.
I can't say I've noticed skipped time stamps but I haven't been looking for them anyway.
Well done on your progress with Lady Heather though. I hear she can be a cruel mistress (groan)