The “4.4.38” is from the source code version. Anything after that is just a human giving a tag to distinguish some sort of configuration…and to determine where modules are searched for.
When you changed the kernel, you changed what “uname -r” responds as due to the naming tag…not due to source, and not due to configuration…although naming is traditionally changed if configuration is changed (“tradition” isn’t a technical requirement for building a kernel). When you change “uname -r”, you change where modules are searched for. If and only if the “.jetson-v0.1” was an exact match in configuration to the one NVIDIA supplies as “-tegra” would they be truly the same (because then both the source code version and the configurations would be duplicates).
If you look at “/proc/config.gz” while a kernel is running, then it will tell you what the current build configuration is. This isn’t a real file, it is the kernel pretending to be a file and instead showing how it is configured. You would need to run each kernel in turn, save a copy of its “/proc/config.gz”, and then compare them to know how they differ.
Most likely there is a different module in the “/lib/modules/4.4.38-tegra/” versus the “/lib/modules/4.4.38.jetson-v0.1/” directory trees. You might explore those directory trees and find out which modules are in one, but not in the other.