I've been having similar problems with all of my Kobo ereaders for... the last couple of years, at the very least ? I have no problem setting up the reader via WiFi once I buy/reset it and downloading books from my account (most recently with my Libra H2O when I bought it almost one year ago), but after I set up everything else through Calibre syncing via the reader hangs, and I'm forced to use the Kobo Desktop app. I don't use KSM, always update Calibre to the latest version, have no issues otherwise with error messages, importing, losing stats etc. and free space varies from 1GB ca. (my Libra) to 8+ (Glo HD, I changed the internal microSD card). I do patch but the issue presents itself regardless.
I used to ask in the firmware threads if any other people had this issue but it seemed to be only me and I eventually resigned myself to using Kobo Desktop. I don't sync often so it's not a huge issue, to be fair...
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