I've used the split_otu_table.py on the American Gut data when it was at about 5000 samples using a MacBook.
Sometimes, I've gotten this kind of error (or similar behavior) because QIIME detects an extra row in my mapping file. If you've used Excel and currently have a text file, you need to open it as text. If you're working on a Mac, you can do this by opening the file using the File -> Open, and then going through the import menu. Select all your columns as text. (This will make sure you don't have any changes in your mapping file, like inference around zipcode). I think the same is true of windows and Open Office, but I haven't tried it.
Then, highlight maybe 20 cells below your last sample, and delete those rows. I typically to this three or four times, just to be sure. I'll do the same thing with columns.