I am using whatever character settings FTM uses out-of-the-box. I tried changing the encoding in my browser (both IE and Chrome), the generated text seems to be Unicode.
Between uploading a fully-linked tree directly from FTM to uploading a non-linked tree from FTM, I make no changes to any of my settings. Yet the fully linked tree has all Swedish characters displayed as expected and the non-linked tree just shows '?' for each one.
I'm not explicitly choosing GEDCOM, I'm using whatever FTM2012 uses when it uploads a tree from the 'Plan' menu tab.
I will try adjusting my locale from UK to Swedish but as it seems to be using Unicode, I don't see that this would make any difference. Especially as it all works fine when I upload my fully linked tree. there seems to be a difference between how FTM uploads linked and non-linked trees.
My non-linked tree has just names, dates and facts with everything else such as media and notes left out. I wonder if some encoding information is also getting lost/excluded during that upload.