As a rule I don't use the step sequencer much because the last time I tried to make serious use of it I found it problematic to say the least. But tonight I decided I'd have another try, and immediately ran up against something frustrating which may or not be a bug, or maybe just I'm misunderstanding how things work. Here goes:
 
When "Fit To Quarters" is turned on, the velocity bars don't line up properly with the notes in the sequencer. Here's a graphic example:
 

 
Here you can see I have a drum sounding on every beat. But the velocity bars seem to be following their own scale. For the life of me I cannot think of a way in which this would be expected behavior. 
 
If I then turn "Fit To Quarters" off, nothing immediately happens. BUT...if I then enter another note into that row, they immediately jump into the correct slots:
 

 
Have I found yet another stupid, sloppy bug, or is it that I'm completely mistaken and things are working as expected (which is how my "bug findings" usually turn out lol)
 

Are the velocity VALUES correct for each recorded event?  Perhaps it is just some sort of graphic drawing issue.
 
It makes no sense to see velocity bars where there are no actual note events, so I would think those are just incorrectly represented on the draw.
 
Bob Bone
 

Is the number of quarters set to less than the number of beats?  
 
I was able to get similar behavior with 8 beats with a fit to 4 quarters.  However, that's a weird response to a weird request.
 
Honestly, I don't quite get what the point of 'fit to quarters' is.  I read the fine manual and I still am baffled as to why it is even an option.

robert_e_bone
Are the velocity VALUES correct for each recorded event?  Perhaps it is just some sort of graphic drawing issue.
 
It makes no sense to see velocity bars where there are no actual note events, so I would think those are just incorrectly represented on the draw.
 
Bob Bone
 

Well it gets weirder the more I look into it. This is definitely an area of the program that is completely broken. When the velocity bars aren't lined up as above, they do not redraw properly when you adjust them. Oh wait..sometimes they do. But mostly they don't. In fact I can't work out what's going on at all, it's completely screwed. Also, if you add beats to the sequence, the velocity bars get closer together. If you remove beats, they get further apart. I think we can say that velocity bars are 100% broken when you have Fit To Quarters turned on. 

AndyDavis
Is the number of quarters set to less than the number of beats?  
 
I was able to get similar behavior with 8 beats with a fit to 4 quarters.  However, that's a weird response to a weird request.
 
Honestly, I don't quite get what the point of 'fit to quarters' is.  I read the fine manual and I still am baffled as to why it is even an option.

To tell you the truth Andy I don't really understand Fit To Quarters either. I understand that it's something I need to turn on if for instance I'm working in 6/8 and I want each step to represent a certain length. But I don't know enough to work out how to dial that in - I just play with it until it works 
 
Anyway I'm going to file a bug report. 

I would have expected that if I were in 6/8 that each 'Beats' would be an eighth note, and that six of them would make a measure.  You know, like it says in the music books.  However, it looks like Beats is always quarters, so if you're in 6/8 and dial in a 6 beat pattern, it takes two measures instead of the one you would expect.
 
It looks like fit to quarters is correct in that a 3 quarter pattern fills one measure at 6/8.  Good luck with the 7/8 arithmetic.
 
It seems like if beats worked like it should, fit to quarters would be totally unneeded.  I'm curious what the otherworldly explanation for "Yeah, this is how it is supposed to work" would be.

According to the online documentation: "Fit to Quarters will force the pattern duration to fit the specified number of quarter notes."
 
http://www.cakewalk.com/Documentation/defaultJA.aspx?Doc=Music%20Creator%206%20Touch&Lang=JP&Req=Views.14.html
 
I suppose it may be useful for fitting an odd number of beats into an otherwise standard clip length.   Now I'm curious...  OP issue aside, of course. 
 

Step sequencer ONLY uses a meter base of a quarter note.

Right....  so if I have a clip duration of 7, and fit to say 3 quarter notes, I should effectively have an odd sounding result.