arrays elements in strange order

im trying to finish my custom patch but i stumbled on another problem. this time its a bit tougher (at least for me) because i have no clue where the problem comes from. here is the code from the execute:withTime:withArguments method:

   NSUInteger i;
   NSUInteger j;
   NSUInteger connectedCount;
   NSUInteger end=(NSUInteger)self.numOfInputs;
   NSMutableArray *inputs=[NSMutableArray arrayWithCapacity:self.numOfInputs];
   NSUInteger maxCount=0;
   k=0;
   for(i=0;i<end;i++)
   {
      //generate the key string and copy the array to avoid accesing the inputs more than once
      NSString* index=[[NSNumber numberWithUnsignedInteger:i+1] stringValue];
      NSString* name=@"Structure ";
      name=[name stringByAppendingString:index];

      NSArray *array=[NSArray arrayWithArray: [self valueForInputKey:name]];
      if([array count]>0)
      {
         [inputs addObject: array];
         connectedCount++;
      }
      maxCount=fmax(maxCount,[array count]);
   }
   if(maxCount>0)
   {
      NSMutableArray *output=[NSMutableArray arrayWithCapacity: maxCount];

      for(j=0;j<maxCount;j++)
      {
         NSMutableArray *column=[NSMutableArray arrayWithCapacity:connectedCount];
           for(i=0;i<connectedCount;i++)
         {
            [column addObject: [ [inputs objectAtIndex:i] objectAtIndex: j % [ [inputs objectAtIndex:i] count] ] ];
         }
         [output addObject: column];
      }

      self.outputArray = output;
   }
   return YES;

its supposed to merge two or more arrays to one two dimensional array. it seems to do what its supposed to but the order of elements in the output array in QC is messed up. if i give it two structures:

a1 a2 a3

b1 b2 b3

i would expect it to give me:

a1 a2 a3
b1 b2 b3

but it gives me:

a3 a1 a2   
b3 b1 b2

when i look at my code i don't see anything that would cause this. because it preserves the order in the y axis i can presume that i either get the structures mixed up at the start or that the arrayWithArray does it. any ideas?