Kylotan
this just looks like a Sonar bug, plain and simple.
If that were true, I would expect to have seen dozens of threads like it by now, and I've seen none. It may be a bug, but hardly 'plain and simple'; clearly the OP's particular environment is a factor.
I've also seen track templates mess up drum maps quite significantly too.
Drum Maps are a whole different issue. Soft synth MIDI ports are assigned and numbered in the order they're inserted. If the new synth is on a different virtual port than when the template was originally saved, the map is going to be wrong - unavoidable, but easily corrected.