Can you post your savefile?
Also I do believe there's a typo in the secret. Make sure you type it in correctly (even case sensitive)
[Slot 1]
GameInProgress=Yes
EasyMode=0
Entrance=1
HasPracticeBall=1
HasNormalBall=1
HasIronBall=1
HasGlassBall=1
HasSpeedBall=1
HasYogaBall=1
HasJumpBall=1
HasFreezeBall=1
HasFreeBall=1
HasPatheticBall=1
EndingAvaliable=Yes
Balloon=6910
Square=3680
Ah ha, I see the problem. It has to go under the [Secrets] section, like so:
[Slot 1]
GameInProgress=Yes
EasyMode=0
Entrance=1
HasPracticeBall=1
HasNormalBall=1
HasIronBall=1
HasGlassBall=1
HasSpeedBall=1
HasYogaBall=1
HasJumpBall=1
HasFreezeBall=1
HasFreeBall=1
HasPatheticBall=1
EndingAvaliable=Yes
[Secrets]
Balloon=6910
Square=3680