I need help identifying the source of a leak in roof over kitchen extension

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Hi everyone,

I could really use some help identifying the source of a leak. It's in my kitchen at the point where the old exterior wall meets the extension roof (see photo 1). It's a small leak and only appears after heavy rain. And I can hear a slow drip somewhere above where the leak is, again only after heavy rain.

My initial thinking was that the most likely culprit was the flat roof over the extension (see photo 2), so I recently got up there and patched all of the seams with Gorilla Coat & Seal. However, it hasn't worked. I'm trying to think rationally about what might be causing it and what I'll therefore have to do to fix it. Here are the possible causes I can think of. Any advice on which you guys think is most likely would be massively appreciated:

(1) It is actually the seams, but they need a second coat (I didn't put the first coat on massively thick because I only had one tin of the stuff, and it does say on the tin than you might need a second coat). This is the easy option.

(2) It's probably not the seams, but a small hole somewhere in the roof. I can't see any holes, but as you can see from picture 2, water does pool up there in certain places and I'm thinking when you get a lot of rain and it pools to a certain level, it reaches a tiny hole and that's where the water is getting in. Maybe it's worth painting over where the water tends to pool, as that might catch whatever hole it is?

(3) It's not the flat roof at all, but some other source such as degraded mortar in the brickwork letting in water, which is soaking down to where the flat roof joins. I am sceptical about this because the brickwork (see picture 3) seems in fairly good condition, including where the flat roof joins the main structure. And, the felt joins the brickwork at a gradient, so there's nowhere for it to pool at the join. Also, just feeling the bricks, they don't feel particularly wet, so I would be surprised if that amount of water was making its way to the kitchen via that route.

Then again, I have no clue because I'm a new homeowner and all this DIY stuff is new to me! Also just to note, I've been in the loft and can't see any signs of a leak from the roof over the original structure.


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That windowsill doesnt look in great shape either above, or the brick mortar.
Maybe it's worth me trying to patch the mortar around the window before I get any more serious work done. Would that just be a case of looking out for degraded bits of mortar, digging it out, and replacing with fresh, all round the window?
 
I’ve got everything I need to do the job and tomorrow should be sunny so I’m going to have a go. Couple of quick questions though for anyone who’s done repointing before.

I’ve noticed a few strange things about the existing pointing, which you can see in the pictures.

Above our front window the perpendicular joints look empty except for a bit of what looks like sealant. Would that be for a specific purpose or would I be okay to fill them in? And should I try to remove the sealant?

I also noticed at the side of our patio doors there is a horizontal joint that has a piece of wood in it. Again, is there any reason not to remove the wood and fill with water?

And then above the patio doors at the back, there are no weep vents, or at least they look like they’ve been filled in. Is this a worry? I have noticed that the wallpaper in the interior alcove for the patio doors has peeled, which makes me think there’s damp (although no mould and it doesn’t feel wet at all).

Any help is much appreciated.
 

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