Are you using a composite primary key, i.e. a primary key with more than one column? The reason I ask is that the OM - 0.7.1 template has some support for composite keys, but the other three templates do not, which would explain the difference in behavior when using MySQL 5.x.. However, last I checked, the composite key support in that template was incomplete. (Disclaimer: I'm not the author of that template; my answers can't be considered authoritative.)
If that's the case, you have a few options. If you have control over the database schema, you could use a synthetic primary key instead. Or, you could write the .hbm files yourself. NHibernate does support composite primary keys, even though they're not recommended. Finally, you might look at
http://www.objectmapper.com, which is another (recently) free tool that has some support for generating NHibernate mappings. It's slower and not nearly as customizeable as MyGeneration, and the class files it generates leave something to be desired in my opinion, but when I looked at it a few months ago, it was a little better than the existing MyGeneration templates at handling odd database schemas. It might do composite keys; I don't know.
If that's not the case, if you're not using a composite key, can you post the table schema and .hbm.xml file that's generated from the 1.1 template?