The gain/input sensitivity of amps can vary quite a bit. Could be the separate amp you are using for the sub simply has more gain than the amp being used for the speakers.
As noted earlier in this thread, the Schiit SYS is a $49 passive preamp that you could use to adjust the volume of the sub. Simply put it inline in between the sub amp's input and the source output.
Also, remember that subwoofers are extremely sensitive to their placement in a room. Too close to corners or a wall/floor boundary can increase their loudness, particularly at certain frequencies. You might try moving the sub further away from a corner or wall placement and see if that helps. And this particular experiment is completely free!