Got it resolved by adding quotes around the table names. The old ODBC driver wasn't picky on that, this one is.
I was having this problem as well with Apache Cayenne and FMP11.
For me it was strange, some objects failed on select and some did not, there was no particular reason why a specific object type would never let me query, it just would not and it failed with FQL0001/(1:25). It was consistent though (Object A always failed)
In Cayenne 3.0 the devs added a 'Quote SQL Identifiers' option at the map level. Selecting this fixed it!
Thanks nateborland, this was a satisfying end to a 4 hour ordeal.