The Toradex Windows CE BSP supports milliseconds for RTC. Normally, functions like GetSystemTime return the time where the millisecond part is always 0. When enabling the millisecond feature, these functions will return the time including milliseconds. This could be used e.g. for timestamps.
[HKEY_LOCAL_MACHINE\Time] "EnableMS"=dword:1 ;enables the millisecond feature.
On the IMX6 BSP milliseconds are automatically supported starting with image version 1.0beta4