I am really sorry to hear that you are having problems updating the firmware.
We have recently discovered that if you upload the firmware to the board using the AVR ISP programmer, you can not upload the firmware via USB after. It is quite surprising because you can configure your board with the Smart Uploader instead.
This is, you can configure your board using the Smart Uploader on the web platform but when it comes to upload new firmware (or new firmware settings) using Arduino’s IDE it will always give you this annoying red message and the subsequent console text.
When I started configuring this batch of SCKs we used an Atmel AVR ISP programmer to burn the uploader and also to upload the firmware. Luckily, after few boards programmed using the AVR ISP we realized of this issue. Unfortunately, some of this few boards were shipped on the run and it seems like you have one of them.
All this uploading issues can be fixed burning the bootloader again and uploading the firmware ALWAYS via USB. I am afraid the reset button does not help in this case.
Burning the bootloader is a quite simple operation but you need a ISP programer as the Atmel AVR ISP Mk2 (http://www.atmel.com/tools/avrispmkii.aspx). Or you can also use another Arduino as an ISP programmer (http://arduino.cc/en/Tutorial/ArduinoISP).
Bootloader corruption problems is one of the most common issues we are facing so we are already working on a tutorial (among many others) on How to use and Arduino as ISP programmer with your SCK. We hope to have it ready ASAP.
As this is entirely my fault, I will take good care of providing you all the necessary documentation and assistance.
My most sincere apologies for any inconveniences this may cause.
I look forward to hearing from you.