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.
"It's inexcusable for scientists to torture animals; let them make their experiments on journalists and politicians." -Henrik Ibsen