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CCS/LAUNCHXL-F28069M: CCS/LAUNCHXL-F28069M: Running from FLASH, working code but motor response not the same as RAM based code

Part Number: LAUNCHXL-F28069M

Tool/software: Code Composer Studio

I copied the LAB13c  code, customized the encoder code, added buffer logger for charting, for various testing and customized the PLAN, and so on. The code worked perfectly in RAM. 

I now moved the code into FLASH while marked the code "CODE_SECTION/ramfuncs" to be copied from FLASH to RAM that is related to ISR loop. 

I run the motor code which spin in accordance to PLAN (38 turn spin CW and 38 turn spin CCW) and found the spin performance was poor compared to 100% RAM code.

I'm running out of idea on how to fix this issue. I checked the labs document and could not see advice.  

I'm guessing the "inline void ST_runPosPlanTick" and similar code everywhere in Ti library with inline would automatically go to RAM from FLASH without the need of "CODE_SECTION/ramfuncs" statement?

I'm going to check 15KHz ISR loop timing via GPIO toggle just to make sure, I'm open for suggestions?