As one user posted in blog feedback, it can be utterly aggravating when your flowchart acquires jagged lines. It's remarkably easy to get into this state. I don't know about you, but I end up with jagged lines when I start to resize shapes while maintaining connections. Let's say that I'm using the Basic Flowcharts stencil. If all my shapes are process shapes, it's often no problem to create and maintain the flowchart. Throw in a few decision shapes and a terminator shape, and things can get ugly. The problem is that almost all of the other flowcharting shapes have less room for text than the process shape. In order for me to fit even a small amount of text into the shape, I have to resize shapes. When I resize, I can run into problems with jagged lines. When I first started using Visio, I'd get so aggravated that I'd end up deleting the offending shapes and recreating the flowchart with a new layout. Since then, I've discovered some neat tricks to fix my problems without generating re-work.
Here's some trouble-shooting steps that you can walk through to fix the problem.
1. Zoom and nudge: The most common action I take in Visio is to zoom. Use Ctrl+Shift+left-mouse-click to zoom in and Ctrl+Shift+left-mouse-click to zoom out. I zoom into the problem line area at about 250%. Then I click the shape and using the down keyboard button, "nudge" the shape down (or maybe up) to see if the line snaps into place. I might do the same for the line too. If the line jumps around in different configurations or I can't nudge it into the right position in about 30 seconds, I go to step 2.
2. Align shapes: I select the two (or more) shapes that aren't connecting properly. I then go to the Shapes menu and select Align Shapes. There are two options in the resulting dialog box: Vertical Alignment or Horizontal Alignment. Pick the option that maps to the flow of your shapes (if your shapes run in a horizontal or vertical line).
It's a little more complicated if you are trying to align shapes that are not entirely vertical or horizontal; for example, a decision shape that has four options but only one of the options has a jagged line. Then you would want to select all the option shapes underneath the decision shape (in other words, all the shapes that you want aligned at the same level) and align those shapes horizontally as a group. If that doesn't fix your jagged line, you can try to align the decision shape and the problematic option shape as a vertical line.
Regardless of which alignment I choose, I always select the setting option that has the line running through it. 
You should also select the checkbox that says "Create a guide and glue shapes to it." This option drops a dotted line guide to which your shapes snap and stay. It's a lot easier to align new shapes to that guide and to move shapes around it.
Every flowchart is different, so you might have to play around with it a bit. In the examples that I've tried, I've usually either fixed my problem with aligning shapes or gotten close enough with the alignment and guide that it takes one more nudge to fix it. For example, sometimes I might have to select the connector lines (as opposed to the flowchart shapes) and align those to sort out my jagged line problems. It might get me close but require one extra nudge to push into place along the guide line. Overall, though, when I align all the shapes at a given level, as I’ve done in this example, it results in a much more attractive layout and NO JAGGED LINES.
Hopefully, this helps smooth out jagged flowchart lines. Let me know in feedback or comments if you're still stuck.
-- Mai-lan
This posting is provided "AS IS" with no warranties, and confers no rights.