Here is a photo of the tomato seedlings.....

More photos....

I am thinking it is one of two things:
1. Some sort of fungus or virus
2. Something to do with the cooler nights and hot days?

Your first post shows zone 6 but not after that for some reason. Did you change it? Where in zone 6 are you located as I am in zone 6 in SW Missouri and temps two nights ago it got down to 25 F. Under a low tunnel/hoop house it will be that same temp inside. That is a real bummer! Hope someone else chimes in with more suggestions.

Zone 6, south central Kentucky ~

It has dipped below freezing recently, but it's been so warm during the day -- it was really hot in the hoophouses yesterday and today so I vented them.
Perhaps overwatering?
It seems like if it were soil related that my other raised beds would be having the same problems---bu they seem very happy...

is this your first experience in a hothouse???

too hot during the day stresses the plants.. each plant individually.. you cant compare between types ...

cold at night is worse ... again.. no comparing between types ...

i would never use wood as dividers.. as there is no way to sterilize it.. and things happen when wood is laid on wet soil/media ...

when the media gets too hot.. or too cold .. then plants react differently ... some will get extremely stressed .. certain temps are required for germination.. and some are requisite for continued growth of the seedling... until they are mature enough to thrice.. regardless ...

what i think you are finding.. is that germination is the easy part ... and growing on.. a vast number of plants.. can get really tricky .. i am thinking there might be a greenhouse forum ...

but all that said.. with all those variables to perfect.. it would still be a long jump... for me to move to disease .... and remedies ... as a cause ... rather than an effect ... of your problems ...

if in fact.. some such arose.. it is most likely ... due to the cultural variables above ...

its still extremely early.. remove the uglies.. and plant more.. in a different spot ... by the time they come up... hopefully spring will also arrive.. and moderate all the temp variables ...

ken

ps: is that growing media.. or compost??? .. as in not a professional product ....