Lines Not Converting From Autocad to Pdf

I am using Windows 7 Pro, Autocad 2011 (full version), Acroplot Pro 2013 and Adobe Acrobat Pro.
Using Acroplot Pro, we convert Autocad files to pdf. We are having issues with some lines, or entire sections of a drawing, not converting to pdf file. As if someone erased random lines from the drawing.
I've walked through this process with Acroplots help line and they say it's not on their end. I know the issues has nothing to do with Autocad because I can re-do this process and the pdf will come out fine the 2nd time. It's rare and random, maybe one file per 100, but causes a problem when you're converting hundreds of files and don't know which one may be wrong.
Thanks in advance.

Sorry if I was unclear, we load our cad files into Acroplot which then utilizes Adobe Acrobat Pro claims it's an issue with Acrobat Pro to create the pdf. After walking through the process with Acroplot, they say it's an issue with Acrobat Pro.

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