Problems with Transparency? Part 2

First, I would recommend using a generic for loop, ie, pairs. That will reduce your use of list[i], which happens a lot.

function AdvancedLoad()
	local programs = game.Workspace:GetChildren()
	for _, program in pairs(programs) do
		if program.Name == "Program" or program.Name == "SProgram1" or program.Name == "SProgram2" then
			local modelparts = program:GetChildren() 
			for transparency = 1, 0, -0.01 do
				wait()
				for _, v in pairs(modelparts) do
					v.Transparency = transparency
				end
			end
			for _, part in pairs(modelparts) do 
				for transparency = 1, 0, -0.01 do 
					wait() 
					for _, v in pairs(part:GetChildren()) do 
						v.Transparency = transparency
					end
				end
			end
		end
	end
end

Now, I see there's a repeated chunk of code that fades out. We should probably make that into a function:

function fade(model)
	for transparency = 1, 0, -0.01 do
		for _, part in pairs(model:GetChildren()) do
			part.Transparency = transparency;
		end
		wait();
	end
end

function AdvancedLoad()
	local programs = game.Workspace:GetChildren()
	for _, program in pairs(programs) do
		if program.Name == "Program" or program.Name == "SProgram1" or program.Name == "SProgram2" then
			fade(program);
			for _, part in pairs(modelparts) do 
				fade(part);
			end
		end
	end
end

Perhaps this makes what's going on clearer? I think it's odd/suspicious that you use fade on program and then again on each of its children... Is that the issue?

You didn't describe the problem very specifically, so I don't really know where to look.