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sorry for the long delay. Fortunately I can bring some light in the situation.
The freeRTOS time is based on a low frequency external crystal oscillator with 32.768kHz. One tick period is 1 ms. There only occurs a 1-2% tolerance between two ticks. Depending on this the timer ticks of the XDK are measured stable.
Therefore the described issues can have another reason depending on the used tasks. The issue with the SD card example occurs with the additional runtime of the application. This parameter can also be configured in the logfile of the SD card. Therefore both runtime of the application and sample rate of the sensor conclude to the occuring timestamp of the measurement. This implicates the discrepancy of the timestamp accuracy.
For more information about that issue you can find the proper explanation here.
I hope this brings some clarity.
Kind regards, Franjo