2.0.1 compile rtf or word loses indents

I have a 100,000 word novel in Scrivener that I just compiled using a custom format, to have it as arial 10 pt, with single line spacing. I chose compile for word. When I exported it, I found that the paragraph indentations are fine at the start of the manuscript, but they get lost somewhere between a third to a halfway through and it just becomes one long chunk of text unbroken by indentation or line breaks. Compiling in the novel manuscript template on the other hand seems fine.

I did search the forum before posting this and noted that this comes up as a problem with Scrivener for Mac when exporting to word. I did the fix suggested there and chose compile for rtf instead, but the same formatting problem reoccurred in rtf as in word.