Seriously, there is no excuse for a sequencer app to still have these type of sync issues in 2012:
 

My newest project.
 
How do I avoid these issues?
 
 

What sync issues?

Check the image I updated it with.

So, the picture shows what I always seem to run into. I run into these sync issues where the clips are not all matching up on the measure lines.

um. change the clip lengths.

I think you're assuming that "we" know what you're talking about.

You're not being clear here. Some things that would be helpful to know in addition to just having a screenshot:

1. Which clips are you expecting to be in sync?

2. Did you record all those clips at the same start time (example: multi-tracked drums)?
3. Are you sure you didn't do any editing to the clip start times after the fact?
4. What were the steps you followed to create the issue?
5. Can you reproduce the issue?

Preferences > Snap to Grid > 

Uncheck the "Snap to Nearest Audio Zero Crossing" box.

I never have anything selected less then a 1/4 note and the pictured scenario occurs when I copy and paste clips. The clips are trimmed exactly by the snapped measure.
 
 

Are you sure you have "snap to" selected as opposed to "snap by"? 

Yup, it's set to "snap to" measure. Sorry, for being obscure with this, but I can't seem to be able to explain it in words. So here is what I was trying to show in the screenshot. The cursor/playhead is set exactly to the measure, tracks 1-3, 5, 8, 12, and 17 all seem to be off, behind, by something between 49:01:000 and 49:01:001. I just want it to snap to these markers if it's set otherwise I just can't count on the sync.