CAN taking Near 100% of CPU

Question

I have been on this problem for a few weeks now and still unable to fix the problem:
Description of the problem:
1- When reading from 2 CAN channels with a Real-Time PXI Controller, the Processor runs between 70% and 80% (but most often at 80%). (Nothing else runs on the RT, but it will be required that more vis to run on it in the futur.) When running the vi on the Host PC, the processor on the RT controller tops at 100%. Some Data loss occurs.
2- Minor problem:  Board doesn't always reset even with 2 resets.)
 Program Content (view attachement for more details):
 1- While Loop at 2500us containing a sequence structure to read 2 Canbus ports in sequence. To read the CAN, I use a ncGetAttr (Read Entries Pending) followed with a ncReadNetMult.v. Data is then unbundled and set into an array in order to use a shared variable (using Real-Time FIFO). This alone takes 80% of the CPU LOAD.
2- First sequence: Canbus Reset.vi. Second Sequence has the Config (set at 1MHz), Open then CActions of Reset and Start.
Description of Task:
Read 2 CAN channels from a UUT on a Real-Time PXI Controller (8196). 16 CAN frames per whole CAN Message per channel. The 16 CAN frames are sent in 2.5ms. The Host PC that reads the data from the Real-Time Controller at any rate (I usually set it at 4 times the loop time of the RT Target).
FIFO Configuration:
12 elements of the CAN frame + RT TickCounter. As 64bits Double or 64 bits U64. 13 elements per array. 512 Arrays (this number varied alot). The lower the # of arrays, the more random data loss occurs, but the higher it is, the more the duration of data loss is long. Note that sometimes i get the last frame and appears in the log as many times as loop size.
Host PC:
Reads the Shared Variable in a For Loop with the #the same as the FIFO size (or higher). 
Note: Many Disable diagrams, but doesn't affect the program in any way. Its other tests done.
Thank you. 
Attachments:
CAN Channel 1 vi.JPG ‏186 KB
CAN Channel 2 vi.JPG ‏187 KB
CAN Config vi.JPG ‏173 KB

Answer 1

Thanks for the replies, I fixed the loss of data, but not the CPU load by doing the following:
I finally tried Queues on the RT (didn't earlier because it was way too slow to execute when I was running my simulation on Windows). I based my vi with the NI Example Queue basics.vi. I also optimized CReadMult, I send the Data direclty into an array with I insert the Tickcount* then send it to the Host PC for it to process the rest of the frame building and then to process the information. Doing both (Queues + CReadMult) helped since now I do not have anymore loss of data, however the CPU LOAD goes up to from ~75% (at start) to 87-89% and stays there.
*Tickcount: I've noticed a weird effect with the Tickcount: I'm sending the msec time and the loop which adds it to the array is set at 2.5ms, however the tickcount read at the Host PC is always on a 10ms timer difference (instead of ~2.5) which also seems to correspond to the same loop timer as the secondary while loops that all they do is sent the information to the Host PC.  The priority of the CAN loop is 1 and the priority of the SV loops are 100. Unless i'm mistaken, priority 1 should be of highest priority and 100 is lowest (excuted only when CPU has "extra" time).
With the Queues: 
Currently it worked (without data loss) when both CAN channels are read in sequence with 2 different loops to send the informatiosn to the PC through shared variables. The RT FIFO is set at 32 Arrays of 2048 Elements. 2048 because the CReadMult seemed to have been going up really high randomly. I have not had the time to optimize the RT FIFO or really know how to cound it exactly. When using the size indicator of the Queues, they are always full. I only use Enqueue and Dequeue.
@O_Proulx:
CReadMult seems to be the main problem of the dynamic array since the information gotten from the CAN seems to vary alot. Are you saying I should insert the data from CReadMult into a fixed array size before sending it through the SV ? I don't think that would help since it seems that the CReadMult automatically creates dynamic arrays.
 @Caleb:
Like I said previously in this post, I stripped everything down, even the bitwise operations of CReadMult to do them on the Host PC. I'm using the NI PXI-8461/2 Series 2 2-Port High-Speed Can. Next time I get time on the benchtest, I'll verify the CPU Load time when removing the SV loops.
Thanks.