File Size Problem with EyeFi SD Card and Arduino Mega
After some testing and research, I found out that the Eye-Fi SD card starts a transfer once a file reaches 20kb or more and will not upload a file again once it has been transfered already.  The solution, as suggested by ChrisStratton, is to log to a temporary file and trigger a transfer once the file is ready.

I took advantage of the fact that the Eye-Fi only transferring files in the standard camera folders.  In my case, I used the Nikon naming convention: DCIM/100NIKON/DSCNxxxx.JPG  (xxxx is the photo number ranging from 0000 to 9999), but there are also others.  Check on the Eye-Fi website for compatible cameras.  I created a temporary file called TEMP.TMP and stored it to the root folder of the card and logged to it.  Once I'm ready to transfer the file, TEMP.TMP gets renamed to "DCIM/100NIKON/DSCNxxxx.JPG" and the whole file is transferred all at once.

Here's my code.  I'm using the software serial (pins 10, 11, 12, 13) of the Mega:

//Running with 256kb serial buffer (modified HardwareSerial.cpp)
//Added file time stamps

#include "SdFat.h"
#include "SdFatConfig.h"
#include &lt;Wire.h&gt;
#include "RTClib.h"

#define SYNC_INTERVAL 1000 // mills between calls to flush() - to write data to the card
uint32_t syncTime = 0; // time of last sync()

#define ECHO_TO_Serial     1 // echo data to Serial port
#define WAIT_TO_START      0 // Wait for Serial input in setup()
#define MESSAGE_SIZE      11 // Message size of "!G N +1234" + CR
#define SOFT_BUFFER_SIZE  256// 25 Messages of 11 chars each

const uint8_t chipSelect = 10;

SdFat sd;
SdFile logfile; //create log file

RTC_DS1307 RTC;
DateTime filedate;

uint16_t date;
uint16_t time;

int i = 0;
int x = 0;

char directory[] = "DCIM/100NIKON";
char filename[] = "DCIM/100NIKON/DSCN0000.JPG";
char tempfile[] = "TEMP.TMP";

/*************** ERROR ***************/
void error(char *str)
{
  Serial.print("error: ");
  Serial.println(str);
  while(1);
}

/*********** TEMP FILE CREATION ***********/
void newFileName()
{
  sd.chdir("/"); //check DCIM/100NIKON directory
  // create a temp file 
  for (uint16_t i = 0; i &lt; 10000; i++)
  {
    filename[18] = i/1000 + '0';
    filename[19] = (i/100)%10 + '0';
    filename[20] = (i/10)%10 + '0';
    filename[21] = i%10 + '0';
    if (! sd.exists(filename))
    {
      Serial.print("New file name: ");
      Serial.println(filename);
      break;  // leave the loop!
    }
  }
}

/****** call back for file timestamps *****/
void dateTime(uint16_t* date, uint16_t* time) {
  DateTime now = RTC.now();

  // return date using FAT_DATE macro to format fields
  *date = FAT_DATE(now.year(), now.month(), now.day());

  // return time using FAT_TIME macro to format fields
  *time = FAT_TIME(now.hour(), now.minute(), now.second());
}

/*************** SETUP ***************/
void setup(void)
{
  Serial.begin(115200);
  Wire.begin();
  RTC.begin();

  if(! RTC.isrunning() )
    Serial.println("RTC is not running");

  // set date time callback function
  SdFile::dateTimeCallback(dateTime); 

  // initialize the SD card
  Serial.print("Initializing SD card...");

  // see if the card is present and can be initialized:
  if (! sd.begin(chipSelect, SPI_HALF_SPEED))
    error("Card failed, or not present");

  Serial.println("Card initialized");

  // see if the directory exists, create it if not.
  sd.chdir("/");
  if( !sd.exists(directory) &amp;&amp; !sd.mkdir(directory) )
    error("File directory not created"); 

  // create new file name
  newFileName();

  // Scan root folder for temp files
  sd.chdir("/");
  while( logfile.openNext(sd.vwd(), O_READ)){
    if( !logfile.isDir() ) {     
      logfile.printName(&amp;Serial);
      if( logfile.fileSize() &lt; 20480 ){
        Serial.print(" file size too small. ");
        Serial.print(logfile.fileSize());
        Serial.println(" bytes.");
        logfile.remove(); //Delete under sized files
      }else
        if( !logfile.rename(sd.vwd(), filename))
          error(" could not be renamed.");
        else{
          Serial.print(" renamed to ");
          Serial.println(filename);
        }
    }
    logfile.close();
  }

  // create temp file
  sd.chdir("/");
  if(!logfile.open(tempfile, O_WRITE | O_CREAT)) // only open a new file if it doesn't exist
    error("couldnt create temp file");

  Serial1.begin(115200);

  // Rotate the buffer
  for( int j = 0; j &lt; 256; j++) {
    Serial1.read();
  }

  // Look for the '!' character
  while (Serial1.peek() != '!' )
    Serial1.read();

  Serial.println("Logging...");
  Serial.println();

  // Reset buffer index to 0
  i = 0;  
}

/*************** MAIN LOOP ***************/
void loop(void)
{
  if (Serial1.available()){
    logfile.print( (char)Serial1.read() );  
    i++;
  }

  if (i &gt;= SOFT_BUFFER_SIZE)
  {
    logfile.sync();
    i = 0;
  }
}