The case is clear to me. The Airline need to submit a passenger list to Thai Immigration and he is still on the blacklist, hence he got refused during boarding. AFAIK the Blacklist is maintained manuelly by Thai Immigration. Before the implementation of the blacklisting by 1,3,5 or 10 years everyone was marked for life. I suggest the OP goes with a trusted Thai person to Thai Immigration at Suan Plu and ask politely about his father status. No need for Lawyer.
Julia Bassenhoff re student visa it says " each permission not longer than 90days", so they can extend 60days. And the next time 90days. I have seen all kind of scenarios and I do not get the point why they make it so confusing. I have seen Visa 90 days, first extension 60 days, second extension 90 days, next extension 60 days again, than finished, no further extension, get a new visa.....
I wonder what school give 15 month visa? First point to clarify. Second point is, if she plan to fly to Vientiane direct than she has to spend an extra night there.