I solved my own problem by creating another table, looking exactly like the original table. This table loaded the CSV file with no problems, while the former table would not even start reading the file before it issued the error message.
Glad that it works, but I would like to know a bit more about this problem. Versions of MySql and SQLyog? Are the two tables identical? Are they in the same DB? Do they have the same storage type? Did you tamper with my.ini or my.cnf between the two tries?