I've had the same problem with constant rapid-fire alerts that prevent me from doing anything (all program alerts for incoming rather than outgoing traffic). I pretty much wasted $30 calling Symantic tech support. They told me that incomig program alerts are unusual -- program alerts are usually outgoing. Their recommendation was to reset my rules by downloading and executing a file from the Symantic support site. The name of the file is ISRLRSTR.EXE and you can find it by searching the Symantic online support site, which also contains instructions for running it. This tended to make the alerts less common, but did not stop them altogether. So, I run the file once a week or so. I also do not run the program scan to create rules, as Symantic recommends, opting instead to let NIS create them on the fly.
Other things I do on a regular basis that are simply bandaids but seem to help: run Adaware 6.0 and Spybot at least every two days or so. Delete all my cookies every so often. Run registry First Aid once a week. Scan for viruses every night. And finally, when it gets really bad I just drag the alert window as far off the screen as it will go and just ignore it. As the alerts back up my computer slows down, but a reboot will clear the alerts out.
I'm still looking for a real fix for this problem, so if anyone else has a clue what is happening, any suggestions would be welcome.