I know that this post is a couple months old and you have probably finished this project by now, but I figured that there’s probably some other people out there with similar issues so…
While the issue that you’ve described could be due to misalignment, I’m guessing that it’s just an effect cause by aliasing. The shapes you’ve created in InDesign are [b]vectors[/b] – they are made up of absolute points on a two dimensional plane and absolute lines that connect those points. Because of this vector objects can be scaled to whatever size you like without affecting the image quality unlike [b]raster[/b] images which are made up of a finite number of pixels. However, the screen you view these vector objects on [i]is[/i] made up of pixels and when you export a page as a JPEG it rasterizes the image. What does this mean? It means that when you are viewing vectors in InDesign some lines will look jagged and some objects may look slightly out of place because InDesign and your monitor have to render this absolute object onto a fixed grid of pixels.
These misalignments and jagged lines can be diminished by what’s called anti-aliasing; it basically blurs the lines that don’t fall exactly into the pixel grid so that, when not zoomed in, the lines look straight and natural. Unfortunately, anti-aliasing can be very taxing on a computer’s performance so InDesign does not use it while you’re viewing a file. Anti-aliasing is used when you export a file as a JPEG (or as any raster file) and that’s why when you zoomed in on that JPEG the lines looked blurry and misaligned; it’s not actually misaligned, it’s just that the middle happens to be in the middle of a pixel so the middle row and middle column are showing up as a mix of the abutting objects.
I know that Illustrator has a “snap to pixel grid” option (in the Transform panel) to mitigate these issues when exporting vectors as raster images, but I don’t think InDesign has this option. If, for some reason, it is vitally important that all of the point are perfectly aligned to the pixel grid then you should try working in Illustrator or Photoshop, but if what you’re designing is for print then you most likely don’t need to worry about this. When it comes to print, just make sure that any raster graphics you use are at a high enough effective pixel density (aka effective ppi/dpi).
I hope this information helps you or anyone else that may have a similar problem. If you have any questions, feel free to reply and I’ll get back to you if I know the answer.
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