pipes affect vibration?

I put on V&H BSS about 1500 miles ago - never really cared for the sound regardless of baffle, but they sure looked good. For a while I've noticed a vibration at certain rpms - the bike hits some resonance and vibrates, lasts for a range of RPM, then at higher rpm it goes away - it's not dramatic - just annoying.
I couldn't remember if my old setup with the SEII slipons acted the same. Went back to the SEII setup - reprogrammed the PCIII. VIBRATION GONE!
Has anyone else noticed that the pipes and exhaust significantly affect the vibration, both at idle RPM and then at some other resonant RPM?
The unfortunate thing about the BSS is they made the vibration the worst right at where I wanted to be riding - around 40-46mph in 3rd gear, 50 - 56 mph in 4th gear, etc. They are never going back on my bike.
I'm sure I'll get butt-slammed for my opinion herebut I've yet to heara V&H system I like.......
The BSS do look good though
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Yes, I agree 100%. Once I installed the V&H BSS it vibrates around 40MPH in 3rd gear.
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