Once again - a bootloader has nothing to do regarding tuners.
Tuners are controlled by the driver.
It is technically simply NOT possible to watch services from two different transponders with a single lnb.
1.) a single lnb can be set to use horizontal or vertical signal - one direction at a time.
2.) a single lnb can be set to use high or low band - one band at a time.
So it is simply impossible to watch every service just by using two tuners. This is just a wrong assumption which is unfortunatly widely spread.
The only thing what is possible is - to watch services on the SAME transponder. A transponder usually provides several services. That should work.
Transponder 1 provides services a,b,c,d,e
Transponder 2 provides services f,g,h,i
Transponder 3 provides services j,k,l,m,n
...
If you record service c using tuner A, then tuner B is only able to tune services a,b,c,d or e.
Tuner B can't tune services f,g,h,i on transponder 2 or services j,k,l,m,n on transponder 3.
Tuner B is restricted/limited to transponder 1 by tuner A recording on that transponder.
Maybe i do not understand what you write, i asked for a link of your satelite equipment - then everything is maybe clearer.
If you still think it is the bootloader - i will be happy to provide you the old bootlader to flash - but believe me, nothing changes regarding that behaviour.