My novel is broken into scenes. When I compile draft, some of the scenes export as a single paragraph, losing the formatting set up in Scrivener. Not all sections, only a few. Anyone know what I’m doing wrong?
In the compile settings, third tab, are you actually overriding formatting? I’m guessing yes, otherwise there should be no change. Now the next check is to click on any of the scenes that are coming out with bad spacing. Open the Inspector (Cmd-Opt-I) and see if the Preserve Formatting flag is enabled. Now check one that is working. What might be happening is that you have override formatting turned on globally, but only a few documents are set with Preserve Formatting turned off, hence most of your draft comes out the way you formatted it except for a few. If this is the case, it would probably be easiest to just turn off the global override in compile. That tool is so you can write in whatever font and fashion you prefer and then print out a standard manuscript in the end without having to bother with working in that format the whole time.
If none of that is true, an alternative case could be that you have some sections using visual paragraph spacing, and others using actual double-returns between paragraphs. You can test this theory by selecting one of the scenes that is exporting correctly, putting the cursor at the end of a paragraph, and then press the down arrow once. Does the cursor land in between paragraphs or at the first line of the next? Try this test in one of the scenes that is misbehaving and see if you get the same results.
If there is a difference, and the cursor is jumping straight to the next paragraph in the bad scenes, then you have visual spacing set up in the ruler for those scenes. They were probably imported from another word processor or something (or maybe the other way around). It should be pretty easy to fix the problem if this is the case. The easiest way is to use the Find panel in those documents to replace a single carriage return with two. You can input these by using Opt-return in the Find field, and then two of those in the replace panel. After doing that you’ll get a bunch of very widely spaced paragraphs, so you’ll probably want to select them all and use the ruler (Cmd-R) to access the Spacing menu and set them to single spaced.
The suggestions you gave did not work. If I export as an rtf, it comes out correct. But when I change it to Word, whether before exporting or after, the formatting on those pesky sections goes back to one paragraph. What can I do to fix this?
Well if you had said that it actually does work when you compile an RTF, I probably wouldn’t have written 95% of the above. 
It helps to give as much information as possible. For example, what do you mean by, “when I change it to Word”? Are you opening the RTF file in Word and it is fine, but then saving it to Docx or something (in Word) and it gets messed up? That seems very odd to me, so I suspect you mean something else, even though what I just described would be the best way to make a Word document out of an RTF.