Hi Simon
Could be reactivation on a dirty carpet, afterall you are not going to remove all the dirt
Could also be a reaction with a fibre finish, I have one particular carpet in a commercial premise , which always smells for a few days after cleaning and I suspect it's something to do with the carpet.
Last time I texathermed it with no probs, so coluld be HWE causes it.
As for your smell , might be worth treating with a bactericide like Clensan.
Cheers
Doug