Hi Daniel,
A few more things to check:
1) Are your Misc charges attached to a specific Price List Code, or is this code blank when entering order details?
2) Are the Misc charges defined as 'Detail' or 'Total only'? This is on the Misc charge itself and certainly would affect how they print.
3) Are your items (IC or OE) defined with a single segment or multiple segments? We found and fixed an issue regarding printing misc charges and items with single segments, though quite different than what you have run into. The version you quoted in your posting does not have this fix - please talk to your dealer about getting it as it has not yet been incorporated into an official PTF. Also note that this doesn't fix documents already posted, but only those posted after installing the fix.
Regards,