I have not found a limit in size myself in my testing, and I've tried some big imports. Here's what I have seen though:
1) Make sure that if you have a card name that contains a comma, the card's name is quoted. So, for Emrakul you want your entry to read exactly "Emrakul, the Aeons Torn" - quotes and all.
2) If you have special characters, it doesn't seem to be able to handle it. So, you need to put "Aether Storm" instead of "Æther Storm" and "El-Hajjaj" instead of "El-Hajjâj" (there are too many characters to name them all)
3) I can't seem to figure out how to upload files for the duel decks, commander sets or planechase sets right now. If I use the export tool and then re-import the CSV file immediately with those cards in it, the import fails.
Those are the major things I've found. The last one is a bug, I'm sure. I've imported CSV files with those cards in them before. It appears to be that if there are a limited number of errors, the import tool will point them out to you, but if you get many errors then it just throws up its hands and says that your file is busted.