Would you mind checking one thing .. could you run the query after restarting and waiting for the indexes to warm up? I'm wondering if ModeShape is rebuilding its indexes and hasn't yet completed when you're running your query. That's a known issue (MODE-1097) that we're planning to fix soon. Hopefully this is what you're seeing.
I wish this were the case. My test is only adding a single node, and I also run a query by name which does return a result. So I don't think the index to be the cause here.
SELECT * FROM [fincayra:User] as user WHERE user.name='test1'
Okay, thanks. I'm traveling for most of this week, but will look into this when I return. If you haven't already, can you please log a bug report in JIRA?