Illustrator CS6 : Some layers are missing when exporting files

Hello all,
I'm trying to export my project for use in Adobe Director 11, and I'm encountering a problem with the export feature that I believe to be a legit bug, and seeing from the amount of threads related with my problem, I believe some other people have encountered it too. I provided some pics for an easier explanation.
So.. firstly, the image below is the screenshot of my project in AI, combination of paths, mask and pictures.
Next I'm trying to export it to PNG without artboard & use transparent background. Notice that the export preview still shows the image that I expect as the export result.
Below is the exported image.
As you can see, some part of the project is 'missing' in the exported files. The problem still occurred no matter I exported it to png, jpg, even psd. Changing the export resolution and anti-aliasing setting doesn't help.
I've encountered the same problem with different project for at least 5 times in like the last 8 months, and I find that each time I encountered the problem, it can only be temporary fixed by some specific procedures and sometimes each problem won't work with the same workaround. For example, one time I can properly export the project after I copy & paste the 'missing' layers and delete the original layers, in other time I have to select the 'missing' layers, move it a little and then move them back to its first location in order to export it properly. I also find that copying the entire layer that I want to export to a new document works a few times. I can't remember some other solutions I have tried that works, but if these solutions doesn't work anymore, I have to find another and it's pretty confusing since it happen to be 'random'.
Since I believe that this happen to be a program bug, I would love if one of those Adobe guy read this post and direct the problem directly to the AI team or something so it can be fixed in the next updates. Until then, anyone ever experienced the problem? What did you guys do to 'fix' the problem?
Many thanks for people who help me here.
P.S. As I'm writing the last part, exporting my current project to PNG with transparent background seems to be working properly after I tried to export to PNG with white as the background color, I dunno why, but it works now. I still want to know other workarounds to 'fix' the problem though, that could be helpful for other people out there.

The first thing I was going to ask was if you saved as PDF earlier, but then I noticed you specifically said not in your first post. I have lost two layered high res images in the last couple of months due to getting mixed up after exporting to PDF for print. I still don't know how it happened, but I have to assume user error.
I also note you are using CS6 which has the JDI features, so saving as a JPG would not have flaterened the layers. I almost never use TIFF as it feels better to use PSD as it is the native format, and it limits the opertunity to mess up. So I am not being very helpful. If you absolutely didn't save out as JPG or PFD or similar, then you have to start thinking bug, but I have never heard of this happening outside of user error.
[EDIT] Whoops. Overlap. I called for my breakfast half way through typing my answer. Glad you got it fixed

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