That's an interesting question.
I would have guessed that Express and non-Express have the same storage layout, so when you're Googling for other people with similar problems, don't restrict yourself to Googling for problems in the Express version. On the other hand though, bulk insert is a common-place operation and performance is important, so I wouldn't consider it likely that this is a previously-undetected bug.
One obvious question: which is the clustered index? Is the clustered index also the primary key? Is the primary key unassigned when you insert, and therefore initialized by the database? If so then maybe there's a difference (between the two insert methods) in the pattern or sequence of successive values assigned by the database, which affects the way in which the data is clustered, which then affects performance.
Something else: as well as indexes, people say that SQL uses statistics (which it created as a result of runing previous queries) to optimize its execution plan. I don't know any details of that, but as well as "reindexing all indexes", check the execution plans of your queries in the two test cases to ensure that the plans are identical (and/or check the associated statistics).