Sorry to hear about the issue. Just to confirm, you're trying to save an SFrame with 10^7 rows, but it's slow, so you split the SFrame into 10,000 chunks, and the chunks won't save correctly - is that a correct understanding of the situation?
Assuming I'm reading you correctly, can you provide a little more context, either on this public thread, or by email to Dato's support email address? In particular, how big is each row? How many columns, are any of the columns large strings, lists, dicts, etc? What kind of OS and GLC version are you running? Once the SFrame is split into chunks, do all of the chunks fail to save, or just some of them?