Supposedly this brightness will lessen after 100 hours. How many hours do you have on your SP3 and Reference Ones so far? Have you noticed any change in its sound during the time you've been listening to it?
From the third post in this thread:
http://forum.av123.com/showthread.php?s=80bfe619bba9133eb48da61597bb52bb&threadid=98&highlight=100+hours"...they sound incredible right out of the box. Not perfect mind you but incredible. The tweeter is a tad edgy even for my tastes( and I love NHT's) and the midrange is a bit forward and honky. I spoke to Sean [from Onix] and he assured me this will take care of itself in a few hours (about 100) of use."
From the second page of this thread (by Mad Dog):
http://archive.avsforum.com/avs-vb/showthread.php?s=c1e71208067f622c8f08c1e63e058900&threadid=224003&perpage=20&pagenumber=1"Onix Reference 1: approx $1,500/pr
...this afternoon, I found out just how AWESOME these Ref’s are. Simply put, regardless of price, these were the best monitors IMHO on this given afternoon at store 1. All the monitors sounded so good, but the Refs had the tightest, lowest bass and cleanest, clearest sound which I took to be the best accuracy. The soundstage was HUGE. Imaging and depth was amazing as well. They were brighter than the Dyns, but not fatiguing to listen to at all. I did feel they were too bright earlier in the break in period but they have really toned down."
Two counter-arguments to this "it will smooth out" notion: First, our own Mad Dog has stated on AC that the Ref 1s require the components upstream to be their utmost best. So if your front end or cables are not as good as the SP3 or speakers, they may be contributing to the sound you're hearing. Second, while some owners have said the Ref 1s sound great with everything, others have said they're ruthlessly revealing. I only have 5 hours on mine, but they seem to fall into the second camp so far (they're also more forward than my last speakers, which I'm adjusting to). So it's possible you will have to look for speakers that sound good with more recordings, as you posted here. I haven't heard the Von Schweikert VR-1, but the owner reviews I've read seem like they'd make it a good candidate. Same for the Green Mountain Audio Europa, although these are taller, more unusual-looking, and supposedly sacrifice some bass response for a stellar midrange.
Edited to add: Just saw another post which supports your experience of the Ref 1s. From:
http://archive.avsforum.com/avs-vb/showthread.php?s=&threadid=221800&highlight=onix+ref"These speakers are very well balanced. They are very detailed without being harsh. The highs are natural and true to the source. Many of my CDs that I used to like now are made to sound bad because of these speakers."