Are there any differences between command line tools and IDE compilers

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Are there any differences between command line tools and IDE compilers

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Contributor I

I am trying to build a codewarrior 5.9.0 for MPC55xx project using makefile so i am using command line tools. However for the same settings and source file i get two different assembly code for a function

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The IDE's assembly output for this function is 

000014d4 <vDCpu_eAlterISRPrio_Exe>:
14d4: 74 80 06 3f andis. r0,r4,1599
14d8: 71 3f e7 f5 andi. r31,r9,59381
14dc: 7d 29 1a 14 add r9,r9,r3
14e0: 31 09 80 40 addic r8,r9,-32704
14e4: 74 08 07 3e andis. r8,r0,1854
14e8: 35 09 80 40 addic. r8,r9,-32704
14ec: 00 04 00 00 .long 0x40000

And CLT output is :

000014c8 <vDCpu_eAlterISRPrio_Exe>:
14c8: 74 86 06 3f andis. r6,r4,1599
14cc: 70 bf e7 f5 andi. r31,r5,59381
14d0: 04 35 30 05 .long 0x4353005
14d4: 80 40 74 c0 lwz r2,29888(0)
14d8: 07 3e 34 05 .long 0x73e3405
14dc: 80 40 00 04 lwz r2,4(0)

There's a difference as seen and i can't figure out why.

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