As I’ve been prepping my project for the kick off of NaNoWriMo, I went through and unchecked “Included in Draft” for everything that wasn’t going to be made directly into a scene for my novel. Then I saved and exited and went to bed.
Today, I reopened the project to find that everything was back to being “Included in Draft”. So it doesn’t stick when the program is closed, even when saved.
I can confirm this as well using Windows XP SP3. The other toggles (Page Break Before and Compile As-Is) work fine.
I can also confirm this. I am using Windows Vista Home Premium SP2 32 bit.
I also have this.
Windows 7 Professional 64-bit.
I have tried everything. No matter what, when reopened EVERYTHING resets to be included in draft. Whether it is in the Research folder or in the Draft folder itself. I end up going through and changing them all. And then when I re-open I have to do it again. Going to make keeping track of actual word count during NaNo a pain in the booty. I think.
I am re-commenting mainly because at first I thought this was just happening inside the inspector, but it also happens when I change it in outline mode. It doesn’t matter where I alter the value, upon restart everything reverts back to being “Included in Draft”.
Confirming the same thing. However, I also noticed that if you view the word count via Project>Project Statistics or check the Project Targets (Project>Project Targets), the word count is correct as long as that file isn’t in the Draft section, i.e. it doesn’t count the words in the incorrectly-checked files in the Research section even though those boxes are checked.
If you uncheck a box in the Draft section and restart, when Scrivener pops back up the box is checked again it it does count toward those word counts.
Thank you all for reporting and confirming this issue. It is on Lee’s long list! 
All the best,
David
Sorry folks for slow response. I have logged this annoying bug.
Thank you.