Can you confirm that you are using 1.04.00.06 on the target? It looks exactly like the issue that was fixed in the 1.04.00.06 release:
SDOCM00103804: LoggerSM_write2 is incorrect when writing binary data
I looked at the binary data for the LoggerSM binary file. Here is a picture of the contents:
The event record circled in blue looks correct. The 0x02002008 decodes to seq #2 of 0x20 length and it's an event record. The yellow highlighted one has 0x03001808 which decodes to an event record seq #3 of length 0x18. The record is only 0x14 long. The 0x04001808 is the start of the next record. System Analyzer is reading length 0x18 for the yellow one. It then tries to get the next record, but it thinks the first word is 0x5982BFDD (circled in red). It gets confused and fails to process the file.
The fix for SDOCM00103804 to went into 1.04.00.06 was to add the following bolded line into LoggerSM_write2 in the packages\ti\uia\runtime\LoggerSM.c file.
myWrPtr = fillInEventHdr((Bits32 *)LoggerSM_module->sharedObj->writePtr,
numBits8ToWrite, LoggerSM_module->serial++);
*(myWrPtr++) = ((evt) & 0xffff0000) | mid;
*(myWrPtr++) = a1;
If you have an ealier version, you can make this same change and rebuild or upgrade to 1.04.00.06.
Todd