Hi Winston,
I suspect you are looking at the custom keys IMAQdx adds corresponding to System Time when the image was recieved, rather than the timestamp sent by the camera itself (both are available in IMAQdx). I think the system time was in 100ns ticks, but I'd have to look it up to confirm. The Basler cameras definitely use 8ns ticks in their timestamp. They have an attribute you can read that indicates the frequency that should read 125Mhz.
As to which timestamp to use, it depends on your use case. If you only care about relative time between frames over a short interval, the camera's timestamp will be far more accurate because it is recorded in hardware by the camera. If you want to correlate timestamps to real-world time and can deal with some added jitter, the system time may be a better choice.
Also, looking at the image of your VI, I think your timestamp retrieval is still incorrect. You should simply use the unflatten VI with a U64 datatype passed into it (and it configured for network-byte-order). Passing an array like you are doing is unlikely to give you the correct interpretation without doing a lot of re-arranging of the bytes. This is presumably why you see the value truncated to 32-bits instead of 64.
Eric