RTF Report output shows Duplicate or Missing lines

Hi,
We have a program which prints XML output into the concurrent program output file and the output for this file is set to PDF attached to an RTF template.
The RTF output generated should ideally have the output in the following manner
Header 1
- Line 1
- Line 2
- Line 3
- Line 4
Header 2
- Line 1
- Line 2
- Line 3
- Line 4
But, once the concurrent program completes execution, the RTF template displays data as -
Header 1
- Line 1
- Line 2
- Line 3
- Line 4
Header 2
- Line 1
- Line 1
- Line 4
Here HEADER1 section is working perfectly fine. But HEADER2 section shows duplicate lines and line are missing as well.
I checked the XML Output - The data is perfect as required. In case we fetch the concurrent program out file (.out file) and load this into the RTF template offline (in MS Word BI - Addin), and do a preview, the output there too is fine and as required.
I am doubting that the XDO process which merges the XML into RTF template, after the concurrent program generates output, is creating this effect.
Could someone please let me know the reason of this behavior. Is there any metalink note or procedure that we need to follow.
Thanks.

In addition to this, I executed the 'XML Publisher Template Re-Generator' program in XML Publisher Admin resp. The RTF template shows no error.

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