Ive had the same issues. The first time i did a patch panel it was a buttweld with a small but tight gap maybe 1/32 and the weld "sunk" on me about 1/4". I was real worried about using too much filler so I picked up a lead/tin body sauder kit and used that to bring up the worst spots then used a light coat of filler to finish. It was a patch panel about 1'x1' and It took me 4 hours to weld. First tack'd it in, let them cool 15 min, split those gaps and so on every 10-15 minutes id do another set of tacks till it was complete. I also used a damp rag to cool the weld, from what I read now is not reccomended.
Just last week i did two large wheelwell patch panels on my bronco. I decided to get one of those pnumatic flanger tools and flanged the top side of the patch and buttwelded the sides. I also cooled this one with my air hose as I went along. Anyway, my sides turned out great but the top (where the flange is) sunk again. made me want to cry. I thought since it was much thicker it wouldnt sink. I thought wrong. From everything ive been doing to figure out why this happens to me, BE SURE to let the welds cool on there own. And make sure to use a gap the size of the sheetmetal. This is very arguable but in my expierence it seems the tighter the gap or no gap the harder it pulls on the metal around it. It depends on the welder I suppose. I have yet to master this craft of patch panels but I think my heat settings and tack welds are hotter than need be.