I think the reason is that Nick needs more sponsors and the episodes are normally twenty-two minutes long, so they have to cut out things that they deem are "unimportant" to the plot to have more time for commercials.
Buuuut.. it's just a theory. Quite disappointing, though. I feel like I'm missing out.
A warm welcome to you, Sera! Great to see new fans! What you noticed about the Nick@Nite is right, I think. We just discussed this at length in another thread:
http://www.malcolminthemiddle.co.uk/forum/showthread.php?t=2277
Yes, they like to cram as many commercials in as they can, which is really sad, because it's butchering the original vision of the makers. It's not unique to sitcoms. There are a lot of movies running let's say 96 minutes or 128 minutes which were gradually whittled down to more 'manageable' lengths on every rerelease or TV showing. A combination of commercial placement, as you say, easier time slots and sometimes censorship.
When these were restored for DVD release, technicians and original crew were appalled to find out that cuts had even been applied to the film masters, meaning they had to piece together video and audio from various, often inferior, copies they had to search for all over the world.
A similar thing is happening with music rights, meaning companies cannot release a movie or TV series to DVD unless they pay enormous amounts for all the songs they used. This is why only Season 1 of 'Malcolm' is available on official DVD. In some cases, the original songs are replaced with bland covers or cheaper, 'generic' soundtrack music, so what you get to hear for a reissue or DVD release is not the soundtrack that the creators supervised. But that's a different topic altogether!
Luckily, we have the downloads!
Best,
Richard