I did some debugging. I made a smaller table and tested it with Internet Explorer 7. The error is not because of the modified default template, it appears in the default template to. Introducing tpartner's code one command at a time, I narrowed the problem down to this part of the code:
// Wrap each row in a div
// This is kinda verbose but IE won't let me use jQuery shortcuts
var el = document.createElement('div');
el.setAttribute('id','inlineWrapper1');
document.body.appendChild(el);
$('div[name="qRow1"]').wrapAll($('#inlineWrapper1'));
el.setAttribute('id','inlineWrapper2');
document.body.appendChild(el);
$('div[name="qRow2"]').wrapAll($('#inlineWrapper2'));
el.setAttribute('id','inlineWrapper3');
document.body.appendChild(el);
$('div[name="qRow3"]').wrapAll($('#inlineWrapper3'));
Apparently, when this code is run, in Internet Explorer it goes from state A to state B (see pictures attached). Each row appears as a column before its elements, so the elements appear twice with that small red font. After running all the code after the wrapping part, it goes to state C, with the doubles still showing. This doubled code does not appear in Firefox or Chrome, where the table looks great.
Do you have any idea why this happens and how to make Internet Explorer not show these doubled cells?
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State A (before the wrapping):
State B (just after the wrapping) - Variable names and brackets inserted with Photoshop for a better undestanding:
State C (at the end):
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Exported questionnaire:
www.esnips.com/doc/306c4961-ed3a-4a62-a4...1d473b26/test_survey
Javascript code inserted in first boilerplate(b0):
www.esnips.com/doc/470c062f-e6d6-4a38-96...3e9690d93/TABEL-BUN2 
