Since the original issue seems to be on its way to a resolution given that there are only a couple specific projects where it doesn't work, a couple thoughts about MP3.
As noted, if Cakewalk includes the MP3 encoder, they have to absorb the costs. For one program, that's not a big deal. But it's compatible with Sonar, Music Creator, Home Studio, etc. If the encoder was included in every program going out, the license fees would add up to a lot of money for functionality that a) not everyone uses, and b) is available for free in iTunes not it's not essential for Sonar.
Some users like an a la carte approach, some like everything bundled so by definition, one set of people will not like the way it's being handled but the other will. This is why "let's just agree to differ" is the only conclusion that makes any sense.
On an unrelated note, if you do a lot of work with MP3 conversion on a professional basis, nothing beats the
Sonnox Fraunhofer Pro-Codec plug-in. It's expensive (around $400) but it also does AAC, lossless compression, real-time audition of multiple files, surround, difference comparison (i.e., you can hear just the artifacts the MP3 generates), etc. It's overkill for most people, but it's incredibly effective and the functionality is off the hook.