Hi,
I am happy to have found this topic as I am unfortunately encountering exactly the same problem with Spire.
Indeed, when rendering to .wav at low BPM this doesn’t happen.
(Maybe I have to change the genre of music I’m producing 
lol (just kidding))
I am going to further inspect the workaround for this issue (by inserting a dummy note), that has been posted in the other topic regarding this issue First note missing from Render
In meantime I hope, that this issue will get solved by the Renoise developers.