Nope. All the GPS receivers will (should) include the GPRMC string in their data stream. That's the string used by the various GPS-enabled firmwares posted on the forums. No changes to firmware that worked with the old module sold in the Adafruit shop should be required for the newer one mentioned by Adafruit_support.
You may need minor hardware mods if you want to use a different receiver that outputs RS232 (like the BR-335 that I've got - you'll need a simple single-transistor inverter for that) instead of TTL. The connection to pin 2 of the ATmega168V (or 328p) in the clock needs TTL.
Have a look at these threads for lots of info on this specific subject, and keep an eye out for WBP's newest firmware (which I have no doubt he will post in the next couple of days).http://forums.adafruit.com/viewtopic.php?f=41&t=32660http://forums.adafruit.com/viewtopic.php?f=41&t=31146http://forums.adafruit.com/viewtopic.php?f=41&t=25108