If you aren't getting the IVs then you're missing the Standard seed. This could mean that either you are missing your timer0 (not likely if you've tried quite a few times) or missing your target time, or you're not hitting your IV frame. If your IV frame is 1, then that won't be the problem. I'm guessing you're missing your target time, so I'm going to suggest that you try using the 3rd gen. tab of Eon Timer instead of the 5th gen tab, because the 5th gen tab is meant for hitting C-Gear seeds (with delays). If you go to the 3rd gen. tab, set the "first timer" to your target seconds minus however many seconds you're DS is off by (for example, on a DS lite/phat, you have to start the game one second before your target second). This will give you a whole number instead of xx:yy, so I think it works better. Don't worry about the target frame, just put in 0 for that.
You should be using the PID RNG method in the main window, the Method 5 Standard seed will just show you the IVs for each frame. But, since you're getting your target nature, and you don't need a specific ability / gender / shinyness, then you don't need to worry about that either.
You only need to find your parameters once. But if you feel you messed up the first time, you can always try again.