Well, the NPCs don't mess with the IVs you get, just the PID (aka nature, gender, shininess, ability, etc.).
For the amount of spreads you're getting, have you checked how many keypresses it searches through? Right now it looks like you're only letting it go for no keypresses, try allowing one or two. Your frame specifications (1 - 6) look all right, you might want to try something like 11 if you're really needing better spreads.
Sometimes you'll come across months that have pretty much no incredible spreads, so also try looking through more months.
Now, for your Frillish issue... it seems like you're doing everything right. Luck loves you definitely not tonight, lol.
All I can say is, check your DS time to make sure it's exactly what you're going for, and make sure you're not holding extra buttons (and when using keypresses, make sure you hold them as you start the game until the white screen). Oh, and, definitely consider recalibrating in Victory Road using one of your troublesome spreads.