im not sure what a blue square means..
So if you do power+vol up for about 3 seconds while connected and batch tool up you don't get anything?
normally you should get a green square.
I had read about there being a problem changing boot loaders between firmware and that the old boot loader needs to be cleared out first when flashing.
Did you use upgrade or recover?
I think recover is needed in a case like this because it wipes out the flash before writing.
Where as upgrade does a dirty flash (just flashes over whats there)
To be honest im not 100% since im going off what i've read, This is my first android device and haven't tried the new kit kat FW's yet so I've not had to run into that problem.
I had read about fast boot it's suppose to work on the lowest level, a bit of rom, or perhaps a protected space on flash.
In fact I think that's what RKbatchtool uses on the backend, If that's not working I don't know what else there is.
EDIT:
OK so a quick google search shows that Blue square in rkbatchtool basicly means "hey im fucked up"
But apparently is still recoverable.
here's what you do.. open rkbatchtool, load up the firmware.
do what ever it is you're doing to get a blue square.. AS SOON as that happens, hit switch button.. then hit recover.
Hopefully that will start flashing.