Without seeing yor code and having some knowledge of your data it is difficult to establish the exact cause.
Are you specifying a primary index (PI) for your newly-created table? If not, the command will select the first named column in your select-list as your NUPI. This may cause the data to redistribute and (possibly) skew, which could be the cause of your problem.
In any event, if the new table PI differs from that of the the source table, some redistribution will occur.
If the target table is a SET table then insertion could take time as SET tables checks for duplicates and eliminates duplicates while insertion. This could take time. Additional factors might be: Volume of Data inserted. Duplicate Rows fetched in the SQL query.
I agree. Mostly it should be due to not specifying primary index explicitly, By default it takes first column in select as PI. I too did the same mistake some time back, specifying primary index resolved the issue.
Please let us know how your issue is fixed finally.