I'm sorry, I don't quite understand. Let me post what I did step by Step:
Calibration:
Caught 3 pokes and checked the IVs. Obtained a seconds reading of 15 and my delay changed between 494 and 496. I hit 494 more often.
HGSS Prep:
Showed Togepi to Elm
Killed all the roamers
Got Pokerus to the PKMN center
Got all 16 Kanto badges
I then used the Time finder to find an adamant nature. I saved in front of the daycare lady, hit my seed, and gave her the parents. Rode my bike for a while, then the Day-Care man said I had an Egg.
I saved in front of him and checked the egg, it was adamant and male, just like the seed said. Now I want it to get decent IVs. Using the Time Finder again, I found a seed I liked, with a frame of 7. I put that into seed to time and told the program I was using HGSS. It gave me a list of dates and times for the seed, so I picked one. I set the delays to +-30 and +-0 seconds. As I have an Emerald cartridge in my DS, I set it to only display Even delays.
Once I generated, I found my seed, and made my elm calls. Since I had a frame of 7, I made 6 calls. These calls matched up to what I should have gotten, but they skipped the first two calls. I then received the egg, but the IVs were wrong.
Please help!
Your problem lies in the fact that there is an NPC on Route 34, which means if you wait for a bit, he'll move and mess up your frame. You said that when you started calling Elm, the responses were two places higher than expected - this will be because the NPC moved in the time it took you to pause and open up your Pokégear after entering the game world. The reason you got the wrong frame after advancing to the correct frame is because he moved again after you closed the pokégear, but before you started talking to the old man. To stop this, you need to find a different spread on frame 1, so that you can just hammer A as soon as you enter the game world, and hopefully talk to the old man before the NPC can move. Then, using the Adjacent results function of the Time Finder, just look up the IV spread you got, and find which seed and frame you hit - if you hit any frame above 1, unless for some reason you waited for any more than the minimum length of time before talking to the old man (that is to say, if you didn't activate the conversation with the old man as soon as you did on other SRs, for whatever reason), then you should SR, but when the game loads,
do not collect the egg. Instead, wait for however long you feel like, then pause the game and save again. Then retry, and hopefully this time round you'll have saved at a better point so that the NPC gives you time to talk to the old man before he moves. Once you're hitting the right frame (often this will be on your first save), then just keep SRing for your seed as usual.
tl;dr: basically, get a spread on frame 1, mash A as soon as you enter the game, use the timefinder's adjacent results to verify your seed, re-save in front of the old man until you're hitting your frame if necessary (
do not collect the egg before saving), then just keep SRing until you hit your seed, and you should have hit your spread.
Hope I helped :)