Basically, I am showing 10x the number of clicks in my affilite stats than my Adwords reports. The interersting thing is that all of these clicks are unique long trail keywords (I am using keyword tracking). For example, my Adwords stats for yesterday show 500 clicks, and my affiliate stats show 4940. Has anyone experience anything similar?
Is your affiliate link a regular link that might easily be followed by spiders? If so, that might be the cause for your problems too.
At any rate, try to examine your log files if you havn't already done so. They might provide you with some clues that you won't find in adsense and affiliate reports.