Totally confused about phasing

It is more common than one would think but there are many cases where manufactures reversed the polarity.

Krellm7 is right. I experienced this once with a 47 Labs Gaincard amp that was manufactured incorrectly, so it is entirely possible that one of your components has a defect. A speaker cable that is labeled incorrectly could also cause it. A simple substitution with something as inexpensive as lamp cord would tell you if that is the culprit. You may also want to substitute a different pair of interconnects to see if they are the cause.

Since you (apparently) reversed the wires at one of the speakers at random, you might now have both +'s hooked to the minus sides, and vice versa.

Now try switching the connections at both speakers, your imaging should remain the same but you should hear more (or less) bass. If you have more bass, leave them as is; if not, switch them back.

The following can be done to test if speakers are wired identically and will cause no damage to your speakers.

You can easily check if it is your speakers that are miswired. Remove the grill cloth and disconnect the speaker cables from your amp. Take a freash 9 volt battery and touch the cable connected to the black or negative speaker terminal and make contact with the negative terminal on the battery. Now while watching the woofer touch the cable connected to the "positive" or red terminal of the speaker to the positive terminal of the battery. The woofer cone should move forward if wired in "correct" phase and will move backward if connected out of phase. The pther speaker should behave identically. Of course this won't help if the other are improperly wired out of phase in correctly relative to each other but at least will allow you to see if the speaker terminals are at least wired properly relative to the woofer.

I currently have 2 Electrocompaniet EMC-1 CD players and both are out of phase on the balanced connections. I see that you also own an Electrocompaniet. I wonder as you if the manufacturer purposely did this or if it was done when the player was upgraded.