CRIO Poor Performance - Where have my MIPS gone?

I have a cRIO based system that is used to control a motor for a particular application. The application has been developed and enhanced over the years and is currently using about 50% of the CPU. The RT Controller is a cRIO-9012. I have recently been asked to add a 1 kHz (or more) loop function to the cRIO application. I can only achieve a maximum loop rate of about 200 Hz. When I told the customer this, he asked how fast my controller was, to which I replied 400 MHz. “Where is all the CPU power going?”, he asked. He's now thinking of replacing the cRIO Controller with an mbed with C code to get the performance he requires, which is a pity since I'd like to continue developing the application in LabVIEW.
Following on from his question, “where is all the CPU power going?”, I decided to write a simple application to test the cRIO 9012's performance. Below is the code I used to perform the evaluation:
With just the bottom loop running, which reports CPU load over the cRIO Controller's serial port, I have a CPU load of 7.0%. This is the baseline.
I then add the "execution" loops as shown above the bottom loop, one at a time and recoded the CPU load. Here are the results:
1 Loops - 18.3% load (11.3% extra)
2 Loops - 29.4% load
3 Loops - 45.5% load
4 Loops - will not run!
I have two problems/concerns.
Concern 1
The cRIO 9012 has a 400 MHz processor, which has 760 MIPS of processing power. The rate of the simple loop is 2 kHz and each loop takes about 11% of the CPU power. That is, each loop uses up 83.6 MIPS and each loop iteration uses up 41,800 instruction cycles. Where are the 41,800 instructions going? Even if there was a context switch after each loop iteration, this would account for 150 to 200 instruction cycles. Each loop is only doing an integer increment, timing check, compare and branch. These should only take up about 4 instruction cycles (8 if you want to be generous). If this was programmed in C, you could get bare metal performance that allows a single loop rate of something like 40 MHz or with an RTOS something like 2 MHz. Instead, my maximum loop rate is something like 20 kHz.
Where are the "wasted" 41,600 instructions per loop iteration going? This is only 0.5% efficient!
Concern 2
Why does adding the 4th "execution" loop cause the application to halt (or at least not send data over the serial port)?
I like programming on the desktop using LabVIEW and I like programming the FPGA using LabVIEW. The RT Controller is however becoming an embarrassment. Is it really the case that the best additional loop rate I can add to an existing application that already uses 50% of the cRIO Controller's CPU can only be 200 Hz maximum?

Thanks for all the feedback.
MajorTom,
Changing to timed loops instead of while loops makes the performance worse. For 2 Loops, rather than a CPU load figure of 29.4% (22.4% after removing base load) it shoots up to 78.4% (71.4% after removing base load). That is, it runs about 3 times slower, which takes the "efficiency" down from 0.5% to 0.15% efficient.
TimothyA,
I tried making the "execution" loops subVIs (with Preferred Execution System = other 1, with the top level = other 2) and that solved the four "execution" loops problem. Thanks, one of my concerns is now resolved (I'll mark it as such once the conversation quietens down).
The execution time is still large with the 2 loops taking 29.1% of the CPU, which is the same as before.
I tried using the "reduced" us wait next multiple CLN.vi, but it appears to be in LabVIEW 2014 and I'm using LabVIEW 2013. Any chance of resaving it as LabVIEW 2013?
crossrulz,
Thank you for pointing me to the table in the CompactRIO Developer's Guide. I assume you’re talking about Figure 3.5. Priorities and Execution Systems available in LabVIEW Real-Time. I didn't realise that Execution Systems are limited in the number threads (would be nice to get a warning when this happens). This will make interesting reading and experimentation.
All,
I’ve tried various loop limiting rates including Timed Loops and While Loops with RT Wait Until Next Multiple, RT Wait, Wait Until Next Multiple and Wait and the best perform is from the two RT waits. The worst performance was from the Timed Loops.
In summary, I’ve solved the problem regarding how to run more parallel loops, but I still get very poor performance with each loop interaction taking about 41,800 instructions when it “should” take more about 200 instruction cycles. All I want is to be able to run a loop at at least 1 kHz on my cRIO-9012 when I already have an application that takes up about 50% of the CPU. I have the threat of the code being moved to an mbed using C, which I’m trying to resist. Surely a 400 MHz controller can have a 1 kHz loop and not take up more than 10% of the CPU.

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