I know I’m late to the party, but I had the same problem with Adobe Reader on Ubuntu. I’m glad I wasn’t alone and I like that we can use an alternative. Regardless of whatever feelings I may have about using Reader with Ubuntu, I solved this problem accidentally. The one-off is caused by the title page. That’s right. The pretty artwork is confusing Reader and setting the pages wrong for “two-up” viewing.
To solve: View >> Page Display >> Show Cover Page During Two-up. The pages will display the way you want. I thought Reader offered more readable text, but it doesn’t so the choice is up to you.
Sean