[dmforcier]

I do use the towel and baggie method, though I sometime shift to the direct-to-dirt method for some truly recalcitrant varieties (I'm looking at you, C.pubescens) where I sow multiple seeds per cell.

(Now remember, most of my experience is with peppers not toms.)

IME the brown spots are sometimes discoloration from the coat, but I treat it as mold starting and drip some hydrogen peroxide on the area. Some of those seeds germinate normally so don't assume that they have split or died.

Most pepper seeds are flat, with depressed centers. They don't look like they have enough food for three days much less two weeks but they do. Some don't, though, and even when germinated don't have enough energy to break the soil after transplant.

Temperature is important for germinating. I'd say at least 80°F and no more than 90°F. Some varieties seem to like the bed cooler than others. I'll be running along at 87°F and after the eager ones try to jump out of the bag I'll turn it back down to 78-80° when suddenly the superhots starting showing signs of life. Be careful where you're measuring bed temperature as in some configurations I've gotten false readings - false in terms of what the seed actually sees.

When I lay down a baggie I will usually start 8 varieties of at least 6 seeds each (if I have enough). At some point, despite adding H2O2 to keep the mold down you just have to give up and throw the whole bag away. For me that is about 3 weeks elapsed.