Well I started to play with the RTC again today and I made some changes to the application and noticed there was an update to the sketch found here. The Site seems to be down so here's another link to the file DS1307 Sketch.
I've added buttons to read the time/date out and clear/dump the memory to the text box, now it even saves the com port and baudrate settings for the next time you open it up.
Feel free to try it out and let me know if it doesn't work etc. and I'll do my best to fix it.
The software can be downloaded here.