I've got 13.0.1 and this still seems flaky (but maybe I'm doing something wrong?)
I have a tool in the build menu (let's call it "foo"). I created my own Error Regular Expression to parse foo's output, which works nicely (and which incidentally includes a Macro added to the ErrorRE.xml file, as described in error.e). When I run "foo" from the build menu, the first line of output says it's using vsbuild. The errors can be parsed and followed correctly if I double click on them in the build toolbar. But nothing shows up in the message list.
If I run set-error-markers, boom, they are all there.
Only other wrinkle - it was working without the call to set-error-markers for a few tries earlier today. I am of course scratching my head trying to figure out what might have changed. Only thing I can remember doing is adding a context menu for the file type which is input for "foo", and that menu can also run foo by calling a macro which calls
execute('project_usertool foo')
However, I don't see how this could have much to do with it - and in any case, it doesn't work either when called directly from the build menu or from the context menu. However, I will try removing the context menu, but I think that's a red herring...