What type of flux are you using today? - Obviously you have already outlined the difference in the parent materials and parent material preparation, so using the same program/profile will not work; the characteristics are different.
Try increasing preheat time or investing in an inexpensive solder pot and pre-tin them properly. - Was this how the supplier offered/sold them to you? or - did you switch suppliers?
- If they are from the same supplier, I would contact them and asked what changed within their process. They should simply be able to get you properly tinned pins and replace the defective ones.
You certainly could migrate to a more aggressive flux - but to what avail? - I do not know about your final product but I would be wary of changing fluxes so quickly without regards to other processes going on after soldering (eg. Conformal Coatings). Typically you will need to clean the part after soldering if you migrate to a more aggressive flux type. If your team is dead set on creating a "work around" rather than getting the "properly prepared parts", perhaps the first step would be to apply more flux (of the currently used flux chemistry) and increase preheat time. Then let us know the result.
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