It's fairly common to see Division II opponents on Big Sky schedules. Eastern plays an all Division I schedule in 2011, but this isn't the norm. Usually it's one FBS, one non-conference FCS, and one Division II. This is the format we played this year (Nevada, Southern Utah, Central Washington), and it worked out pretty well.
The problem is, the farther west you go, the fewer options there are as far as scheduling FCS goes. Portland State's schedule is pathetic (what were they thinking???) but I don't know the story behind it. That is a very unusual schedule for a Big Sky team, so they might have had someone back out and couldn't get a replacement game with a Division I opponent. Scheduling is difficult, especially at the FCS level. You want to get the right balance of winnable non-conf games that count towards the playoffs, and the annual $ game that most of us have to play. Most FBS games that provide a significant pay-out are not winnable, so if you're scheduling more than one of those in a year you are basically scheduling yourself out of the playoffs. Add a Division II non-counter in there, and you basically have to win all or all but one conference game to make the playoffs at 7-4 or 8-3. This happened to Weber State this year and in 2008 Eastern played two Big XII schools and just missed out on the playoffs because of it. There are a lot of complaints about the 2011 schedule for EWU, but at the end of the day, we opted to go with an all Division I schedule rather than bring in a Division II. Also, when you consider that one of our "home" games has traditionally be played in Seattle anyway (just playing UW at Husky Stadium instead of PSU or CWU at Qwest) then the schedule's not too bad. Not great, but playing all Division I's sets us up best for another run at the title. Not massively excited about playing @ USD, but we will just have to punish them for backing out of the Big Sky.
My understanding is that in 2012, each school will still only play 8 conference games, so don't be surprised if you see conference members scheduling one another for non-conf games.