one of 2 things
Bad connections on the two batteries.
The cables you used are stuffed.
Now this is what I would have done in that position & I'm not recommending you do this.
When hooked to the good battery and as far away from any battery as you can be with the length of cable you are using touch the red and black clamps together in a sliding motion, you should get sparks.
If you have no sparks the connections are bad or the cables are bad, move the connections and try again, still no sparks your leads are bad, have a look inside the grips on the clamps you may find a wire has pulled out.
The reason for the sliding motion is so the clamps can't stick together.
Do you know why your battery was flat in the first place ? a bad battery can kill a ECU.
If you don't get positive to positive and negative to negative you will know it, there will be a shower of sparks as you put the last clamp in place, that is dangerous because the gasses in a battery are very explosive, that is why they recommend the last connection is done to the motor not the battery.
Some of the 19 rides in my shed
2014 V2, Snoopy
2009 Wee, Pumbaa the pig
WR450F, The Blue Postie Bike
YZ250N smoker with rego, Stinky.
Yamaha MT09 (FZ09), The Scud missile.
Club Lead not Club Med.
He with the most toys wins.
Out of my depth in a puddle.
Live life on the edge you will see more that way.
Ridding a motorcycle keeps things in balance.
At the end of each trail and at the end of each day history is made.