Just for you to know and for my surprise, it’s been working like a charm since we talk here… anyhow it fails again I’ll try to test without decluttering and report back.
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It just now stopped working… I tried a to capture it as “formatted note” and it worked cluttered and uncluttered. Markdown did not work, with clutter or uncluttered. I try also to capture as plain text and just create an empty note on plain text. After than I try to capture in markdown uncluttered and it worked.
I dunno!!! 
What URL?
I hope it’s not too late to take this one up…
The Best Mac Site-Specific Browser for Google Docs - TidBITS is an example of a URL where Markdown capture failed for me (yielding just a bookmark) whether or not I choose the clutter-free option. All the other capture options work when clutter-free is not enabled; if it is, they too save only a bookmark.
However, my feeling is that this is not related to specific URLs. I had the same problem earlier today with a different website, and restarting DT produced a temporary fix. Now, after failing with the URL above, I’ve restarted DT again and clutter-free Markdown was fine.
DT 3.7.2 / macOS 11.4 / Mac mini M1
We are working on something that may alleviate the need to quit and relaunch. Still testing, but there’s potential.
Thanks @BLUEFROG, and sorry for bringing up a topic that you are already working on. From the discussion above I wasn’t sure of the status of this, but you clearly have it in hand.
No worries at all!
And while we can’t claim it will resolve all capture issues, it may help eliminate (or at least mitigate) quitting and relaunching DEVONthink to clear the problem.