You said you had the stomach flu the previous weekend. Were you vomiting? If so, that is likely a cuase. Stomach acid will eat away at your teeth, gums and lips after vomiting. Enough irritation can cause canker sores. Also, Toolgirl is right, stress will cause this. One summer, six years ago, I woke up one morning to find about 8 or 9 canker sores starting in my mouth. I was barely after to eat or talk for about a week. I had very bad teeth at that time and the tension in my mouth was bad enough to cause a frequent canker sore here and there. However, I had a lot of stree on me that summer and it took its toll in my mouth. I went to a doctor who tested them (probably for Herpes but I'm not sure) and the tests all came back clean. He pretty much said "We (doctors) don't know why canker sores seem to pop up for no reason. Get some more rest and try to lighten the stress in your life." Btw, the test does not feel good. He took a long cotton swap (cue-tip) and dragged it across all the sores and then pushed down hard into the biggest sore. Not a fun experience at all. My sympathy goes out to you for dealing with this. As a side note, I haven't tried this but I have heard and read that an old remedy for canker sores that appears to be true is to rub your own ear wax onto the sores each night.
Forgot to add: I've also heard that some doctors speculate that if your body has just fought off a virus (perhaps a strain of the stomach flu) that the virus may mutate before being completely defeated and manifast as a canker sore.
-DAGTA