HAH!

I found the problem thanks to the help of some users on the MySQL forum. I noticed that the server was upgraded to version 5 which I'm assuming happened on Thursday. I actually noticed this by accident when I was double checking the version of MySQL so I could put it in my post on the forum. I had a sneaking suspicion that this could be the problem, but I wasn't sure. Then a user on the forum posted something about using commas in joins. So I checked out the manual and sure enough, I found out that version 5 handles things a little differently. Mainly the below section:

• Previously, the comma operator (,) and JOIN both had the same precedence, so the join expression t1, t2 JOIN t3 was interpreted as ((t1, t2) JOIN t3). Now JOIN has higher precedence, so the expression is interpreted as (t1, (t2 JOIN t3)). This change affects statements that use an ON clause, because that clause can refer only to columns in the operands of the join, and the change in precedence changes interpretation of what those operands are.

  Example:

  CREATE TABLE t1 (i1 INT, j1 INT);
  CREATE TABLE t2 (i2 INT, j2 INT);
  CREATE TABLE t3 (i3 INT, j3 INT);
  INSERT INTO t1 VALUES(1,1);
  INSERT INTO t2 VALUES(1,1);
  

  • INSERT INTO t3 VALUES(1,1);

  SELECT * FROM t1, t2 JOIN t3 ON (t1.i1 = t3.i3);
  

  Previously, the SELECT was legal due to the implicit grouping of t1,t2 as (t1,t2). Now the JOIN takes precedence, so the operands for the ON clause are t2 and t3. Because t1.i1 is not a column in either of the operands, the result is an Unknown column 't1.i1' in 'on clause' error. To allow the join to be processed, group the first two tables explicitly with parentheses so that the operands for the ON clause are (t1,t2) and t3:

  SELECT * FROM (t1, t2) JOIN t3 ON (t1.i1 = t3.i3);
  

  Alternatively, avoid the use of the comma operator and use JOIN instead:

  SELECT * FROM t1 JOIN t2 JOIN t3 ON (t1.i1 = t3.i3);
  

  This change also applies to statements that mix the comma operator with INNER JOIN, CROSS JOIN, LEFT JOIN, and RIGHT JOIN, all of which now have higher precedence than the comma operator.

So after making one of the problem queries compliant with this, all was well.

Now I just have to upgrade a shit ton of other queries.