This might not be the problem in your case(s) but I hope it helps. Apologies if it's a bit long winded but I think the context might help in similar cases.
I had a velux window in the garage that had been leaking from a bottom corner for years. The window can have only been opened a handful of times in its 12 year life as it requires a ladder to get up inside the garage roof to get to it!
Like many I believed the window was leaking through the flashings and spent a good couple of hours pooring jugs of water onto various parts of the window to identify the leak. Only when I gave up on the flashings and ran water down the frame (not the glass) did I see water ingress (not immediately, only after a couple of minutes).
The leak turned out to be in the frame roughly in line with the central hinge, barely visible (covered by the upper bits of the frame) it looked like a bit of collected mud but was actually a bent bit of aluminium. Watching the two aluminium strips (one fixed, one moving) that
overlap the glass edge, as the window was opened and closed it was clear that the moving piece had dug a hole in the frame, probably on opening during installation!
To cure this I removed the moving strip (two screws) and trimmed the hinge end of the aluminium with a pair of side cutters. I cut the side corner of the strip off at about 30 deg from its long edge, quite a gentle slope and rounded it off with a file. On reassembly the corner on the upper face then dug itself underneath the edge of the frame and forced the whole thing down into the frame (perhaps the real cause of the problem). So... I then also trimmed the corner on the upper face at about 45 deg and again rounded if off with a file (I may have also taken about 5mm off the length). When reassembled I checked that there was at least a couple of mm clearance from the frame over the whole range of movement.
Having allowed the whole lot to dry thoroughly I cleaned up the aluminium frame and pressed the bent bit back flat with a screwdriver. With the aluminium strips off (out of the way) I used a 150mm (ish) piece of flashing tape slid as far in towards the frame as I could manage and pressed down with a flat bladed screwdriver to seal it up and then replaced the aluminium strip. (On final, final reassembly I also used a tiny amount of gutter sealant in the countersinks of all of the screws as there is evidence of water damage to the wood frame from the tiny bit that leaks in here!)
The other side of the same window was digging its own leak but had not gone through yet, similar treatment was applied. Our other 5 velux windows now all have a note to NOT open them until I've had a chance to check them out. The garage is now completely dry, despite some heavy prolonged rain.
Unfortunately I haven't got round to sketching this up or photographing it. It's fairly obvious once seen but if anyone's really stuck I'll try to draw up what I did and/or take some pics.