Speakers sound too bright.

"Ignore the app. Make sure the amp’s positive (red) terminal is connected to the speaker’s positive terminal and the amp’s negative (black) terminal to the speaker’s negative terminal. On both speakers. If one speaker was connected backwards, the bass is out of phase and will cancel out."

Maybe not. Maybe the app is correct and one of the speakers has reversed magnetism? This does happen and I have a professional JBL woofer like this which is reported by one of their authorized service reps as happening for about 1 in 50 woofers!

I just couldn’t get the two woofers to phase properly when connected the same. I discovered that when a compass is held up to the front of the two woofers, one shows north and the other shows south! YEAH THEY DO!!!

Or maybe the wires are crossed inside the cabinet and the external connection would appear correct?

A 1.5 volt battery is probably the best way to check.

To rule out a speaker being wired incorrectly internally and assuming you have your speakers hooked up correctly, just play tracks 22 and 25 from this — no need to mess with resistors and such. Left should be left, center should be center, and right should be right and if all that lines up your phase is fine. I continue to think it’s break in, but you should consult your dealer to get their thoughts as well.

http://www.youtube.com/playlist?list=OLAK5uy_ndrls3SVVIl_vwa6lSQILyH7DnQGCevqg

While checking internal and external wiring for correct phase is always a good check (noting internal wiring checks a difficult task that may void warranty) and out of phase wiring will potentially cancel or reduce bass output, cause potential, perceived brightness due to lack of base, it also produces a characteristic hollow sound and incorrectly wide staging effects.  I recommend you check but do not consider this a probable root cause if you are not hearing the characteristic hollow sound and staging effects.  

If you had speakers in the same room that sounded good to you, return the speakers.  I had the same issue with B&W 702 S2 towers.  The dealer told me to burn them in for 100 hours.  4 days later they sounded the same.  I returned them.  Life is too short.  A lot of good speakers available that will sound good to you in your room.  Suggest buying from a dealer or direct from manufacturers that will let you buy, try and return if necessary.  

I had the Motion 40's (same tweeter) and then the upgraded AMT tweeter (bigger) in the ML 35XTi, which was a good bit better that I could not go back to the Motion 40's.

The tweeter in the newest ML, the B100 (which is way more expensive) is the "gen 2" tweeter (35Xti being the first generation). The B100 has the "waveguide" built into the cabinet, but otherwise it is the same size. I could not hear a difference between the 35Xti (that I still have) and B100 I heard at Best Buy. 

I only bi-wired my 35Xti's, using Audioquest Type 4 or 5. If the manufacturer goes to the expense of adding a second set of speaker terminals, I see that as a sign that it does increase performance.

It certainly is not your DAC. I have an Yggy and it is not bright. Would suggest leaving it on all the time though. If you ever feel the case of the Yggy and its slightly warm, it will sound best. 

Someone mentioned using a better pair of tubes that came with your Preamp. That will help a lot. Probably should have done that before switching out your speakers as it makes a difference with all speakers. The JJ tubes that came with my Rogue RP-1 were far inferior to the NOS Mullards ($120 a pair) that I replaced them with. Most noticeably in the upper frequencies.

Your room, not treated, certainly has something to do with your perceived brightness. In fact, that may be where you could make the most difference using the least amount of money. 

I love AMT tweeters. But I generally listen to soft dome with a pair of Wharfedale Linton Heritage Speakers. Since AMT is relatively new to market (90's when the patent expired allowing the technology to be utilized by many- and blossomed in the 2000's) there is (as someone stated) a wide margin between low dollar AMT speakers and high dollar AMT speakers. Hence, if I had my druthers, I would have a pair of Wharfedale Elysian's (5K and up) which have a super AMT tweeter instead of the Heritage with soft dome I listen to now.

IMHO, the ML 35XTi with its AMT Tweeter provides better highs than the soft dome on the Linton's- at a far lesser price especially if used - but with the Lintons everything else is better mid-bass, bass, cohesiveness..etc. But AMT tweeters - good ones - really are a treat, especially with expressive tubes in the Preamp outputs.