Historically, the following four table have been interpreted the same was, as a two column table with an INTEGER PRIMARY KEY in the first column:

CREATE TABLE t1(x integer NOT NULL, y test, PRIMARY KEY(x));
CREATE TABLE t2("x" integer NOT NULL, "y" test, PRIMARY KEY("x"));
CREATE TABLE t3([x] integer NOT NULL, [y] test, PRIMARY KEY([x]));
CREATE TABLE t4('x' integer NOT NULL, 'y' test, PRIMARY KEY('x'));

However, in 3.9.0 and 3.9.1, the t4 table above is interpreted as a two column table with a separate PRIMARY KEY index on the first column. Hence, if the database schema above is created with version 3.8.11.1 or earlier, then PRAGMA integrity_check will show an error with version 3.9.0 and later.

Version 3.9.0 and later should interpret all four tables above the same way.