About the spurious 0s in your data - look carefully at what you're doing! I think that the problem is that you always put something in the queue, even if there is not a full CAN packet to read from the FIFO. Try moving the Enqueue into the case structure.
Don't put obtain queue in the loop - each new obtain queue opens a new reference that you never dispose of, which will lead to steadily increasing memory use. Just grab the queue wire from the obtain queue outside the loop, and branch that into the upper loop.
The TDMS issue is much easier than adding a for loop. Remove the for loops and array manipulation, and wire the mode (terminal at the top of TDMS Write) to be "interleaved" instead of leaving it unwired which causes it to default to "decimated."
EDIT: also, there's no need for the 10ms timer in the bottom loop. As I mentioned previously, the dequeue will handle timing because the timeout is unwired - it will wait until there's data available, however long that happens to be. Once you fix the upper loop so that it only enqueues data when there's a CAN packet to send, this should work well. However, you may want to move the Release Queue function to outside the upper loop or otherwise work out the timing because as I have it, if no CAN packets are received then it won't exit when you hit the stop button because the queue will continue waiting forever. Releasing the queue causes any queue functions that are waiting on it to complete, returning an error saying the queue reference is no longer valid. You may want to handle that error in some way because the dequeue will also return an empty array, which you won't want accidentally added to the data file.
