Yes, that is exactly the problem. The file I posted is basically the originall ldc_GeoTrans_TNR3.conf from the samples but I changed the resolution so that input and output are different from each other.
That should work right? According to the Documentation there are no resolution requirements when combining GEOTRANS and TNR3. But it seems that src and dst need to have the same resolution so that it does not return an error. The question is, is this a bug or a missing detail in the documentation?
Please make sure to reproduce the issue with the input file that matches your input surface/rectangle settings, and then provide everything (the command line, the config file, and the input file) for us to look into the issue.