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FTP: I as an example own many hundreds of domains (have owned thousands). Keeping a list completely up to date would be a burden, and would likely burden you own systems down. Whitelistings domains is a good way to a certain extent, but it can cause other issues and create work.
Part of the process of tracking, regardless of IP address, is to use all the tools that are at your disposal.
1 - Trace IPs... hey, why not?
2 - Build your tours with "pass forward" tracking devices on all clicks. Don't pass the affiliate code forward, but rather some other form of coding (so that it cannot be easily replaced by malware that replaces affiliate codes).
3 - use phpsession or similar type arrangements to track users within your systems.
4 - don't assume a user coming to your front page is a new session - check for an existing session for this user. That is the fastest way to avoid cookie / affiliate code write-overs.
5 - check to see if you have been framed / Iframes / img src'ed.
Combining those things together, plus other tools will normally allow you to keep track of a surfer right through your system, and also help you to identify and eliminate traffic leaks. The "pass forward" method on tours is particularly powerful, especially with a coded tracker, as it will really slow down code-replacers.
Variances between these things, comparing shifts in IPs, session variables, pass forward tokens, and even surfer cookies combined will give you some powerful tools to look for data slippage and loss.
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