Indices on the new table will slow down an insert, all else being equal. Delete those (if present) and you're likely to see and improvement. If that doesn't help, it probably means that the select was the rate-limiting step (hope that phrase makes sense outside chemistry and enzymology) so you should check your select more carefully. For example, change subqueries to joins, where possible.

Of course, the right answer is the Explain as suggested earlier but here are a few other suggestions if the results too confusing.