I actually just figured my issue out, not sure if it will help you. I have a True/False field in the underlying data that I converted to 1/0 specifically so I could do conditional formatting. Apparently when that data pulls into my report, it shows as -1/0, making the 1 a negative. No idea why it's doing this.
So I just added a new column which multiplied the value by -1 and voila, my conditional formatting started working again. Maybe it's something weird like that?