Remember that our ears loose a lot of "memory" after about 3 seconds. So unless you were able to switch back & forth between those 2 different hookups, then the "loss of bass" could be in your mind. Im not saying that is what happened but unless you had the wiring wrong, there is not really much else it could be.
If you have an SPL meter then you could place it on a stand about 12" in front of the drivers of one of the towers. With the master volume unchanged, get the readings with each of the 2 wiring configurations. Check to see if there is any difference in output. Make sure all settings are identical & the meter is not moved.
I have my sleakers bi-wired & it made no difference in sound AT ALL!!! i could have saved myself $ on wire & connects had i known. Haha oh well, live & learn
Now, bi-amping, with seperate amps with seperate power supplies can be of benifit but even that is debatable depending on the speakers & power involved.