[XSleeper]

Hard to help with no photo.

 

[XSleeper]

Water runs downhill. And the installation instructions for shingles specify the amount of stairstep that each course makes. So if you follow the mfg instructions, water is not going to be able to seep over (for example) 7" before it runs downhill 5".

This assumes the shingles are not installed on a low slope roof, which would increase the likelihood of a leak.

 

[XSleeper]

Would need to see the sides of the skylight. There should be step flashing on every row. Looks like someone already gooped the hell out of it. You typically never caulk the bottom edge of a shingle or flashing. All that will do is act like a dam and cause any water under there to back up behind it.

 

[XSleeper]

No, stepflashings do not need sealant at the seams. Its a real diy move to just go caulking everything up with tar... it just creates a mess. Typically a roofer who is going to stand behind his work would want to replace the skylight with a new one that comes with a flashing kit. Not surprising that no one wants to do it.

 

[XSleeper]

Of course there is. Water can get under your shingles where they meet the skylight on the side. And you've caulked the bottom edge of every shingle so that water can't get out. So it will obviously be wet and maybe muddy under the shingles. It could very well be that the entire problem is because of that caulking.

 

[XSleeper]

Yep, that is the thing to do.