I still don't get it, man. What the hell are you talking about? It can't be skipping calls. If it skips calls, you are doing something obviously wrong. Which calls does it skip? Your problem is that you are counting, simple as that. You DON'T need to count. As soon as you enter the game, you'll open the pokegear and see the Roamers position. If it matches the one you needed, you get your seed, input it on the first screen of RNG Reporter, select Method Breeding (HGSS), and click generate, with the roamers on the routes they were when you saved.
Then, you skip the first frames, as they were skipped (they are the roamers frames), and start counting from your start frame (RNG Reporter will say what it is to you, no problem).
Then, you call once, and see if it matches the ELM column on the RNG Reporter screen. If it matches, you go to the next line. Call again, see if it matches.
And you do it until you are one line above the one with your IVs. Then you get your egg.
I can't explain it to you more clearly, so I hope you get it now.
Edit: No, there are no missing calls. If you don't exit the pokegear screen between each call, the frame can't be skipped. There is NOTHING that can advance your frame while you are inside the pokegear, unless you have something playing on the radio. Anyway, if there are frames missing, as you say, it's because you didn't hit your seed.