Hi Eden Li,
I found the issue. The SQRT implementation used in the toolbox is faulty. The “MC Toolbox for MPC564xL v1.3.0” from the web contains a very old Beta release rev 0.91 of the Automotive Math and Motor Control Library Set (AMMCLIB) for MPC564xL (released in 15. August 2011). In the mean time, some of the issues were fixed and the latest available AMMCLIB RTM release v1.1.8 (available for evaluation purposes via web http://www.nxp.com/automclib) contains a fix for the issue.
All you have to do, is to download the v1.1.8 and then to copy-paste 4 files from the v1.1.8 into the MPC564xL v1.3.0 installation folder.
The files needed to be replaced are:
GFLIB_Sqrt_SF_FLT.c
GFLIB_Sqrt_SF_FLT.mexw64
GFLIB_Sqrt_SF_FLT.mexw32
GFLIB_Sqrt_SF_FLT.tlc
Those files can be found in the v1.1.8 library under ..\bam\GFLIB\bam_flt\ folder and should be copy into ..\rappid564xl\MCLIB for MPC564xL\bam\ folder
You should get this result.

Hope this helps!
Daniel