I have also experienced the same issues.
I gave up checking the spam folder for legitimate comments because I almost never found any. When you do a search using what looks like the legitimate comments, you will likely find out that they are also spam.
Don't worry about finding false positives in the spam folder. If you are using Akismet, that does not happen very often. Just focus on moderating the comments awaiting approval. I find that about 80% of those are also spam.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin