I detailed the issue I am having here:
http://stackoverflow.com/questions/38330348/continuous-error-21-library-routine-called-out-of-sequence
I have since narrowed it down to a piece of code. This passes:

    TEST_FIXTURE(DatabaseFixture, TryToCreateATable)
    {
        database db(test);
        CHECK(db.exec("CREATE TABLE test (id INTEGER PRIMARY KEY, value TEXT)"));
    }

But this fails (normally it is REQUIRE CHECK(db) but I removed it to make sure it isn't REQUIRE causing issues).

    TEST_FIXTURE(DatabaseFixture, TryToCreateATable)
    {
        database db(test);
        CHECK(db);
        CHECK(db.exec("CREATE TABLE test (id INTEGER PRIMARY KEY, value TEXT)"));
    }

The db boolean check is

operator bool() const { return connected_; }

If you replace the CHECK(db); line with the following:

if (!db) std::cout << "Not connected! " << db.error() << std::endl;

It passes. You can see the bool operator is called by placing a cout in there just to acknowledge the call.

While I initially thought it was Sqlite3 related it appears it is the boolean operator causing the issue.