If some conversions are missing, firstly try widening the time range of reporting, since FunnelFlux Pro attributes conversions to the time of initial entrance from the traffic source.
So for example if a visitor arrives on the 3rd Jan and goes to the offer, logs their hit ID there, and converts 4 days later on the 7th Jan, the conversion will appear in the reporting for the 3rd Jan, since it attributes to the entrance time.
This may seem a little odd, but its done this way so that your time-based reporting properly reflects your ROI based on your traffic, so that ad spend and revenue aligns --> giving you correct ROI data for different days and hours.
Next, check the hit IDs that are being passed to the offer/affiliate network. Only offers can convert, and all offer hit IDs end with an "h". If you are passing hit IDs for a lander, they won't be eligible to convert.
If neither of these is the issue, let us know and we can investigate further.