If you look at the first line in the progress dialog (the one showing output of the merge), you can see that the one that doesn't work for you shows "respecting ancestry" at the end, the one that works has "ignoring ancestry". So, since you're merging from the same url you have to check the box "ignore ancestry" in the merge dialog as well. The log dialog does this automatically since merging there is always from the same url.
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