I have made this post into a video, its a lot easier for me to explain it this way.
Please see the link below.
http://www.youtube.com/watch?v=Xwp1ZzylNEE
This problem has started to happen on our 2007 RC also, but we have figured out that just turning it off then back on seems to solve the problem.
All this started to happen right around the time where we implemented Kevin’s ADC code.
If anyone can help us with this problem i would very much appreciate it.
This is very strange… But not too strange.
I notice your use of Vista. That could be problem number one. Try getting a machine with XP loaded onto it, and installing a fresh copy of the loader. My guess is that your problem has something to do with how Vista is handling your COM port.
Just a guess.
Jacob
This definitely smacks of a communication problem, rather than a problem with the IFI hardware. I would recommend trying either a different USB/serial adapter or a different computer, and see if any of this behavior changes.
Ah yes, I forgot about the adapter… I replaced all of our programming machines with P3 laptops with REAL COM ports on them 
The VEX cable works best.
Jacob
I have tried this with both a REAL com port, running windows XP, the usb -> Serial adapter running windows xp and the adapter running vista… all have the same problem.
I had it working for a while after i posted the video, might have sent code about 10 times or so and then it just stopped working half way through a download.
Is there a possibility it has something to do with the timer interrupts in the code or something like that?
Its been over an hour now since it has worked.
Dashboard works fine through the usb to serial adapter.
But I am still having problems with programing it.
Last time it stopped working was in the middle of a transfer. This has happened before and i solved the problem by leaving it unpowered for 10 mins or so then re-connecting it. It by default goes into program state and i send it code.
Not working this time around. It fails to connect every single time.
Its doing this from a PC with a serial port too.
I have tried holding the program button down while powering it on, (which turn on only the power led and the program led) and i still have the same problem.
I am 100% out of ideas right now
Have you tried a different serial cable?
Maybe your batteries are low, causing the microcontroller to reset.
Check your 12v and backup.
Yes i have tried a different serial cable, 2 diferent ones actually… not only that but they all work fine on dashboard.
The batteries are fully charged. just came off charge this afternoon and they havent done anything but run the rc.
Next time that it decides to cooperate with you, I would recommend re-downloading the Master Code, and then downloading the default code again. I’m curious if it might be a firmware issue.
Where can i get a copy of the master code?
It not looking promising as to co-operating again… its been a long time now…
Im currently seting it up to try it on my desktop.
http://www.ifirobotics.com/docs/frc-master-ver15.zip
If you haven’t tried reloading the firmware before, then I wouldn’t be all that surprised if this fixes some of your issues.
Update:
Same thing on both my Desktop through the serial port and the usb to serial adapter.
I have also emailed IFI, Anybody know how quick they are with responding, i know its the weekend and all, but we only have 3 weeks left.
Make sure you have no other programs using the data port (like dashboard). Make sure you are using the right COM port (using device manager).
is there any way to reload the firmware without using IFI loader, as it will NOT connect to the RC anymore at all.
and yes i am sure that no other program is using the port.
and i have checked in device manager to make sure i am using the correct port. I have even tried changing the port, rebooting and it still doesn’t work.
we had this exact problem!
We fixed it by either
A) hold down the prgm button while powering up the RC then when the first 2 leds light up release try to download
B) press download and while it is trying to download put it into program state…
(requires good timing but worked every time for us…) 
hope this helps
Just tried both of these options, still no luck.
hmmm im out of ideas have you tried to contact FIRST about the issue?
I’d try letting it sit overnight, and re-downloading the master code in the morning.
I have not yet contacted FIRST, but I have contacted IFI, no response yet.
I am suspecting that it has something to do with the code we are uploading to the RC. as everything was working fine until we started messing with interupts and kevin’s ADC code.
hopefully IFI get’s back to me soon, and if I don’t hear from them by monday, i will contact FIRST as well as call IFI.