Sakamonda, I'm sorry to hear about this. We share the same agent and I'm enduring the exact same submission process that you are now undergoing. I got the wierdest neg comment from Ann at Bantam Spectra for "not pushing the genre enough." Other than that I got all As for the other parts. And believe me, I hate it when I near-miss a perfect publisher.
The only problem that I can think of is that maybe your man was too over-the-top. Personally, I'm hoping that the trend changes in the future where the mysterious, badboy, brooding, control-freak, domineering type get his azz thrown out of the script, and is replaced with the strong, aggressive, winner, type guy, tempered with just the right sensibilities and satire. Did you give him a personality quirk, or something to showcase the humanity in him? I only say this because the cliche', indestructible alpha male can be a bit one-dimensional, and certainly predictable.
However, I'm male and no romance writer. So I would wait on any additional comments from future editors and see if you can glean a trend from this. But this is...puzzling because Desire leans toward this type of male character.
Hang in there. We're going to make it.
Tri