If replacing the rcS by the original file does not help, I do not know what to do. One last idea: There are two linux partitions on the SD card. One is the system partition and one is the recovery partition. They have similar content. Are you sure that you are copying the file to the system partition? Since you were comparing the file dates with the 2.6.1 FW and they are corresponding in several cases, I guess you are dealing with the system partition. So this seems not to be the problem. That your on-animator.sh has a different date seems to indicate that you have KoboLauncher installed, this is not part of the problem.
Maybe a new image is the best idea now. For later analysis an image of your current sd might be interesting. But I guess you don't have the time and mood to create one.
For creating and writing flash images, I find these tools very convenient under Windows:
http://www.vconsole.com/client/?page=page&id=28
http://www.vconsole.com/client/?page=page&id=29
I am sorry to be not able to give you more help.