Filer warning of creating multiple files even though only one is created

I'm using the Apt tool with a custom program that I wrote to autogenerate some Java classes for my project. Unfortunately, the Filer is throwing a warning. Even thought the below code is only called once, I get a multiple create warning. Any ideas what's causing this?
Mark McKay
Filer filer = env.getFiler();
PrintWriter pw = filer.createSourceFile(indexClassName);
warning: Attempt to create 'C:\dev\cvs.kitfox.com\scarlet\gen\com\kitfox\scarlet\\Index.java' multiple times

I disocvered that this error was coming from the fact that my processor was being called twice - once for my original soruce files, and then again to process the file I had just generated. Once I handled the case of the reentrant call to process(), I was able to avlid this warning.

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I have uploaded the files and shared them. These are the links
Grade 11 Maths Standardisation Project Paper 2 2013.doc
https://files.acrobat.com/preview/9694310d-ca7f-4919-883d-c53b36215d89
Grade 11 Maths Standardisation Project Paper 2 Analysis Grid 2013.doc
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Grade 11 Maths Standardisation Project Paper 2 Formula Sheet 2013.doc
https://files.acrobat.com/preview/7fc6007b-aaa6-4d65-9a8c-bf99818474a5
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https://files.acrobat.com/preview/b3a715bb-3683-48df-b0ec-3d17442275be
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https://files.acrobat.com/preview/ab62e6b6-0261-434e-8a2f-382f74335685
The first file is the problem file. If you create this file separately, Acrobat will convert it perfectly. But "Batch create multiple files" and the graphics are deconstructed on page 8

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I have uploaded the files and shared them. These are the links
Grade 11 Maths Standardisation Project Paper 2 2013.doc
https://files.acrobat.com/preview/9694310d-ca7f-4919-883d-c53b36215d89
Grade 11 Maths Standardisation Project Paper 2 Analysis Grid 2013.doc
https://files.acrobat.com/preview/97da9e5f-d412-4d25-9bbc-d1a525d90826
Grade 11 Maths Standardisation Project Paper 2 Diagram Sheet 2013.doc
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Grade 11 Maths Standardisation Project Paper 2 Formula Sheet 2013.doc
https://files.acrobat.com/preview/7fc6007b-aaa6-4d65-9a8c-bf99818474a5
Grade 11 Maths Standardisation Project Paper 2 Marking Guidelines 2013.doc
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Grade 11 Maths Standardisation Project Paper I Analysis Grid 2013.docx
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The first file is the problem file. If you create this file separately, Acrobat will convert it perfectly. But "Batch create multiple files" and the graphics are deconstructed on page 8

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I have uploaded the files and shared them. These are the links
Grade 11 Maths Standardisation Project Paper 2 2013.doc
https://files.acrobat.com/preview/9694310d-ca7f-4919-883d-c53b36215d89
Grade 11 Maths Standardisation Project Paper 2 Analysis Grid 2013.doc
https://files.acrobat.com/preview/97da9e5f-d412-4d25-9bbc-d1a525d90826
Grade 11 Maths Standardisation Project Paper 2 Diagram Sheet 2013.doc
https://files.acrobat.com/preview/f50dd62e-af04-4060-85c5-fa81ce6803d8
Grade 11 Maths Standardisation Project Paper 2 Formula Sheet 2013.doc
https://files.acrobat.com/preview/7fc6007b-aaa6-4d65-9a8c-bf99818474a5
Grade 11 Maths Standardisation Project Paper 2 Marking Guidelines 2013.doc
https://files.acrobat.com/preview/b3a715bb-3683-48df-b0ec-3d17442275be
Grade 11 Maths Standardisation Project Paper I Analysis Grid 2013.docx
https://files.acrobat.com/preview/ab62e6b6-0261-434e-8a2f-382f74335685
The first file is the problem file. If you create this file separately, Acrobat will convert it perfectly. But "Batch create multiple files" and the graphics are deconstructed on page 8

Filer warning of creating multiple files even though only one is created

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