Some pdfs work others don't

Question

I am working with ApEx 3.0 and BI Publisher standalone on Windows. I have a couple of reports that create PDF's (or other output formats) just fine, but I have at least two reports that comes up with an empty PDF and an error message stating "could not open _file_name because it is either not a supported file type or because the file has been damaged".
I have tried changing to A4/points but this didn't change anything. I took one of the reports, but the data on apex.oracle.com and everything worked. Apex.oracle.com appears to still be on 3.0.0.00.20 so I am a little lost on why the PDF worked there and not here.
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I don't see any errors in the BI Pub application logs and there is no error messages in the PDF if I save them and open under a text editor.
I am sure that it is something silly, but I am missing it right now.
Thanks, Tony

Answer 1

The 3.01 patch helped some. There are still some reports that don't work. The one specific report is a report with repeating header breaks. I'll try to post more specifcs later.
One of the reports that is still failing is a bit complicated. The query for the region contains calls to a functions that return html tables.
select col1, col2, col3,
f_table1(w,x) col4,
f_table2(y,z) col5
from ....
So in this case, col4 would contain an entire html table,
<table><tr>.....</table>
And then in the output, everything is "custom". I only show one column, and use the column formatting to create the entire output. For example.
Column 1 formatting
<table border="0">
<tr style="background-color:lightgrey;">
<th style="text-align:right;">Facility:</th><td>#COL1#</td>
</tr>
<tr>
<th style="text-align:right;">Facility Type:</th><td>#COL2#</td>
</tr>
<tr>
<th style="text-align:right;">Facility Description:</th><td>#COL4#</td>
</tr>
</table>
Whenever I try to print this output to PDF I get the error that the file may be corrupt or in the wrong format.
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T