I'm in an uncomfortable position too, but not "uncomfortable" bad. It's more of an intriguing situation. I know that God led us to the church we're at, but it's different than other churches we've been. They're not as strict with some thing, so things that would've gotten some of our past leaders up in arms, doesn't happen here. The ministry here has a lot of ex-prostitutes, crack addicts, terminal patients, and such. Like I said, it's weird. When I feel like putting on my heathen-detector glasses, God immediately tells me things along the lines of LaRue's second point.
We have to be careful when a leader has short-comings. Sometimes I'll drop an anonymous letter in the church mailbox, as a person that "visited the church recently", other times I'll go and speak to them directly, but which ever route I take, I always watch them and keep my ears open to God, just in case I'm wrong and there is a reason why things are that way.