RS-232 speed different on console vs. window

I have a simple application that I made to test the data rate of a device.  I was having trouble with slow communications with another program, so I wrote this one to test just the RS-232 communications. My problem is that I get vastly different result depending upon whether I compile the program as a console application versus a windowed application.

My device is sending 70-byte message packets at 100Hz using 460800 baud, 8-N-1.  I'm using a USB to Serial adapter, which is supposed to support that baud rate.  Using the console application I get ~7000 bytes/second, which is what I expect.  However, when running as a windowed application,  I get ~34 bytes/second.  Anyone have any ideas about why there is such a vast difference?  (CVI 2013 on Win7)

Code is below.  Inputs I use are:  [COM port number], 460800, 1.

#include <utility.h>
#include <ansi_c.h>
#include <rs232.h>


int main ()
{                  
   FILE * outFile ;
   FILE * binFile ;
   int iNumBytes = 0 ;
   char cMessageArray [720] ;
   int iStatus ;
   int iPortNum ;
   long lBaud ;
   int iByteRead ;
   int iGetRate ;
   char cFileName [20] ;
   time_t timeStart ;
   time_t timeStop ;
   long lByteCount = 0 ;
   long lTimeoutCount = 0 ;
   long lNumSeconds = 0 ;         
   
   
   printf ( "Port recorder.  \nWrites bytes received on the selected port to a file ( {Port #}.txt ).\n\nEnter COM port: " ) ;
   scanf ( "%i", &iPortNum ) ;
   printf ( "\nEnter baud rate: " ) ;
   scanf ( "%u", &lBaud ) ;
   printf ( "\nEnter 1 to just calculate byte rate: " ) ;
   scanf ( "%i", &iGetRate ) ;

   printf ( "\nListening on port %i at baud rate %i (8-N-1) w/half-second timeout.  Press any key to stop.\n", iPortNum, lBaud ) ;

   DisableBreakOnLibraryErrors() ;
   
   iStatus = OpenComConfig( iPortNum, "", lBaud, 0, 8, 1, 8192, 1024 ) ;
   SetComTime ( iPortNum, 0.5 ) ; // COM read timeout in seconds

   if ( 0 <= iStatus )
   {
      // Open output files
      sprintf ( cFileName, "%u.txt", iPortNum ) ;
      outFile = fopen ( cFileName , "wt" ) ;
      sprintf ( cFileName, "%u.bin", iPortNum ) ;
      binFile = fopen ( cFileName , "wb" ) ;
      time ( &timeStart ) ;

      if ( 1 != iGetRate )
      {
         while ( !KeyHit() )
         {
            iByteRead = ComRdByte( iPortNum ) ;
         
            if ( -99 != iByteRead ) // IF not a timeout
            {
               iByteRead = iByteRead & 0x00FF ;
               fprintf( outFile, "%.2X ", iByteRead ) ;
               printf( "%.2X ", iByteRead ) ;
               cMessageArray[ iNumBytes ] = (char)( iByteRead & 0x00FF );
               iNumBytes++ ;
               lByteCount++ ;
               if ( 70 == iNumBytes )
               {  
                  fwrite ( cMessageArray, 1, 70, binFile ) ;
                  iNumBytes = 0 ;
                  printf( "\n" ) ; 
               }
            }
            else 
            {
               fprintf( outFile, "TIMEOUT " ) ;
               printf( "TIMEOUT " ) ;
               lTimeoutCount++ ;
            }  
         }
      }
      else
      {
         while ( !KeyHit() )
         {
            iByteRead = ComRdByte( iPortNum ) ;
            if ( -99 != iByteRead ) // IF not a timeout
            { 
               lByteCount++ ;
            }   
            else
            {
               lTimeoutCount++ ;
            }
         }
      }
      time ( &timeStop ) ;
      lNumSeconds = timeStop - timeStart ;
      printf ( "Bytes = %i, Seconds = %i, Bytes/Sec. = %f\nTimeouts = %i\n", lByteCount, lNumSeconds, (float)( (float) lByteCount / (float) lNumSeconds), lTimeoutCount );

      fflush( outFile ) ;
      fclose ( outFile ) ;
      CloseCom( iPortNum ) ;
   }
   else
   {
      printf ( "Couldn't open COM port!" ) ;
   }
   
   printf ( "\nPress any key to close.\n" ) ;
   
   GetKey() ; 
   
   while ( !KeyHit() )
   {}
   
   return 0 ;
}

Thanks!