First check to be sure you have the correct kit numbers. It's possible that the kit you found is for one or his relatives rather than himself. If you are sure of the numbers, then run each kit through the Diagnostic Utility at the bottom right of your Gedmatch home page. If they are all listed as without problems, run the 1-1 utility with each pair. If you don't get a match at the default settings, lower the threshols to 3 cM and 300 SNPs. Check to see if there are smaller segments separated by only a few cM. That could mean that they are actually a larger segment that has been split by Gedmatch's matching algorithm.
If none of these work, then you seem to have a real anomaly and I would then suggest that you ask your match to contact Ancestry and both of you email Gedmatch at
Gedmatch@gmail.com.