Using the code I gave, no indexes will be created for the new table, so there is no chance of duplicate primary keys being rejected. (You will of course want to deal with that issue later).
Maybe EMS MySQL Manager imposes a limit on the sizes of datasets it can handle. Other MyQSL clients, like the "mysql" command-line program, have no such limitation. Alternatively, you could try adding "LIMIT 9999999" to the end of each SELECT statement.
25 lakhs (25,00,000 is it?) records in a table should be no problem; it will just take a bit longer.