I moved your post to the board on Malcolm in the Middle topics.
I really don't know. Aren't there any repeats? I know, in syndication, programming is often sloppy. I myself couldn't make head or tail of the way MITM was shown on Comedy Central for instance, with some episodes repeated and skipped and some combined into Christmas specials skipping various seasons.
Then there is the pilot, of which two versions exist, one extended, both of which appear on the DVD releases.
I guess the only way is to check screenshots or other media.
I know there can be fewer episodes, which happens when two related episodes are combined in syndication, so when shown by other channels than the original producer.
For instance, "Company Picnic" (3x11 + 3x12), "Baby" (4x20 + 4x21) or "Reese Joins The Army" (5x21 + 5.22).