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If only a percentage of your conversions seem to be appearing in FunnelFlux, here are some troubleshooting steps:

  1. Firstly, check your click loss in general. If you look at your ad platform clicks versus FunnelFlux, are they close? Or are they off my 50%? If only about half of all visits appear, you might have made a common error in Cloudflare in your DNS records, having two competing records for your tracking domain (e.g. an A-record and the CNAME record). That definitely needs fixing if present.
  2. When comparing reports between systems, make sure you know the timezone the other system is using. Be sure to adjust FunnelFlux reports to the same timezone so you're doing a direct comparison. 
  3. If the above is correct, you should see approximate matching between the "offer views" in FunnelFlux vs the clicks/visits in your affiliate network for that offer
  4. If you are able to access click ID reports in your network, which will show FunnelFlux hit IDs, try comparing these to what you see in reporting > raw events in FunnelFlux. Filter to the relevant funnel/source/time and show conversions only. Are some clearly missing? If so, try widening the time range in FunnelFlux and searching again, just in case the network is showing conversions at a different time for some reason
  5. Is the conversion tracking using a postback or Javascript? Postback tracking is quite binary and will generally work, or not. Javascript however is at the mercy of browsers which may block JS, cookies, and it will depend on the robustness of your data passing within the funnel

In general, server-to-server tracking is very reliable, so you shouldn't see much discrepancy.