After spending a frustrating (with amazing F1 in background) afternoon getting GPS to work and updated, I thought it might be handy for anyone that I'd write up a little how-to.
I'm working with FMP04 on Paul's (Flyduino.com) GPSBOB v1.1 and a Sparkfun FTDI Basic (5V)
1. Solder everything up, I started with JST-XT connector soldered directly to the GPSBOB connectors, but switched to regular connectors for software update.
2. Connect wires (I just used one servo-extension cable + jumper cable for GND) to FTDI. Just GND to GND, 5V of GPSBOB to 5V of FTDI (although my Sparkfun FTDI says 3V3, it seems to be a silkscreen error).
!! RX from GPSBOB -> RX from FTDI (same for TX->TX) !!
3a. Get firmware + updater from here: http://flyduino.net/documents/FMP04.zip (10Hz, WaaS, 115200Baud version) !! This is only for FMP04-units bought earlier than 12 July 2012 !!
3b. Get firmware + updater from here: http://www.file-upload.net/download-4231947/FMP04_Camled_010327_A1.5E_20110118_10Hz_115200.bin.html (5Hz, WaaS, 115200Baud version)
4. Unpack files from archive + unpack the firmware tool
5. Start FlashTools.exe
6. In Options menu, select corresponding COM-port and speed (9600, 38400, 115200 or Autodetect)
7. Select DA: 3329 and click Download Agent.
8. Select the corresponding file (MTK_AllInOne_DA_MT3329_v4.02.bin in the FlashTool folder)
9. Click ROM and select the file you've downloaded above (FMP04_Camled_010320_A1.5E_20110118_10Hz_38400.bin in my case)
10. Click Download
11. Watch firmware being cleared (RED) and uploaded (BLUE) and get the (GREEN) circle confirming upload

If you somehow encounter a (RED) cross with an error, please confirm you've selected the right Download Agent and have actually(!) selected the ROM properly.
No need to use the USB_Loader also provided.
For additional options, you might also use the MTK uploader our ArduPilot (and/or DIY Drones) friends refer to: http://code.google.com/p/ardupilot/downloads/detail?name=MTK_DIYdrones.zip&can=2&q=.
Hope this helps anyone!
Cheers,
Ruben
EDIT: Updated download link