Let me note that the ATK/VNL is not based on SIESTA/Transiesta.
The ATK uses rather different algorithms for describing the electronic structure of open systems, and this is why ATK is faster, more reliable and shows better convergence than any other Quantum transport implementation. Technical details are available from our website.
We cannot help with solving bugs in other packages, however, we will be happy to help with any question regarding our own software.
As you might note on the forum, these questions are very rarely related to bugs or convergence problems.