There are different Compilers for Starterware and Linux. When I set the 
flag  -mfpu=vfpv3 in Linux, and Rebuild the project I don't get a different 
result. What I can do in eclipse under Linux is to set the optimizations 
level. What I did yesterday was to change my programm to the following:

double x = 3.1415;

while(1)
{
  toggle_gpio();

  for(i=0; i<35000; i++)
  {
       x = sqrt(x);
  }
}

For Starterware I measured 85,5 Hz and for Linux 19,7 Hz. In both i turned 
off the optimization. This result makes a bit more sense but actually both 
should be the same. The problem with my other programm was probably, that 
the Compiler on Linux saw that I wanted to do the same operation 
sqrt(3.1415) 35000 times and did some kind of optimization even though I 
told him not to optimize. In my new program he gets a new result after each 
iteration of the loop. 
 
But I think I will finish this testing now. In most of my tests Starterware 
got much better results and moreover you don't have the Jitter like when 
you use Linux. 

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