I've noticed that a lot of people are not completely familiar with the quirks of MML so I thought it'd be nice to write an FAQ about it. I'll add to this first post as time goes on as well if I see more questions that get asked quite often.
Where can I learn how to write MML?
There is an excellent guide on the Mabinogi World Wiki that also covers the answers to the questions below. It's pretty in-depth so if you just want to figure out what's wrong with your MML, check the answers below first. If you want to learn everything there is to know about MML and how Mabinogi interprets it, then check out that guide.
Why does my jam's parts not sync up correctly in Mabinogi when they do in 3ML?
The first and obvious thing to check is if your instruments are all playing at the correct tempo. If they are, then you probably ran into a quirk of Mabinogi's MML parser. 3ML and Mabinogi actually parse MML differently. The parser in 3ML behaves how you would expect, but the Mabinogi parser has some weird bugs in it that you have to work around. For this particular problem, Mabinogi for some reason messes up the duration of rests when you put them next to a tempo change; for example, "t100v15r2c". To get around this problem, you can use a silent note instead, like this "t100v0c2v15c".
Why do some notes get cut off prematurely in Mabinogi when they play for the full duration in 3ML?
This is, again, a problem with Mabinogi's MML parser. If you have a track that plays a note, but another track of the same instrument plays that same note in the middle of the first track's note, it will stop the first note to play the second note. So for example, if you have something that looks like this in 3ML:
It will actually sound like this in Mabinogi:
This is only a problem with tracks being played by the same instrument. If you have a flute play the same note as a mandolin, they will not interrupt each other. You can read more about this here.
Why does my song get cut off before it finishes when I play it in game? Why does my song get a ton of extra silence at the end when I play it in game?
Yes, the answer to this question is actually the same. The way Mabinogi detects the duration of a song is very different how 3ML does it. 3ML seems to check if there are still notes to be played, but Mabinogi calculates the duration of all the tracks, picks the longest one, and sets the skill to cancel when that longest track is finished playing. However, the way it calculates the duration of a track is faulty. If there is no tempo specified for the track it's calculating, it won't check the other tracks to see what tempo it should be, it'll assume that the track is supposed to use the default tempo, which is 120. This means that this track's duration will be calculated incorrectly.
tl;dr The easiest way to fix this without too much thinking is to just add the tempo to all parts of the song.
I saw a song being played where the cymbals sounded like a gong. How the heck did they do that?
If you play cymbals at o2d+, you'll get a deep gong sound. It sounds like this: https://dl.dropboxusercontent.com/u/4234581/gong.mp3. Incidentally, the bass drum can also play a note at o2d+ and it'll be a much deeper drum sound than usual.