The blinking orange LED indicates data traffic on the link between the vehicle and FlashScan.
The blinking green LED indicates data traffic on the link between the PC and FlashScan.
There is no significance to the number or length of each flash.

I recommend uninstalling the FlashScan USB drivers and re-installing them. You can go to www.ftdichip.com and then to their utilities page and download a program called FTCLean. That will clean the FlashScan USB drivers from your system. I would post a link but their site is down at the moment.

Then I recommend downloading and installing the latest FlashScan drivers from here:
http://download2.efilive.com/Drivers..._Win-2K-XP.zip

Regards
Paul