I've used Roto Swing Bass on my fives before with no problem, back when my local Sam Ash was blowing them out for $20 a set.
I will tell you that Alembics generally prefer the .128 they're built for (a .130 is an OK substitute), but you can run out of saddle travel once you get up around .135, depending on the brand. 'Piano-end' (taper wound) strings can be a real party, too.
And as David noted, some B's are just not very flexible. This may be a particular glitch in this one string. Next time you buy a set of Roto 5's, it will either happen again, or it may be just fine and never happen again. Up to you as to whether you want to try another set. Occasionally one string in a set is just going to be a problem child . . .
IF you're satisfied that there's no obvious set up problems (binding nut slot or bridge saddle, high enough action to pull it sharp, big relief, really high pickups on the B-side)), for me I'd just play it, I doubt it could be heard in regular playing, unless you've all got VERY good ears. Or just yank 'em, and do something else.
And yes: Any time you replace strings, unless you're replacing with exactly what's on it now, you WILL have to retouch your intonation adjustments, possibly your action if you're sensitive to small changes in feel. A 45 to 125 set of GHS Boomers is NOT the same thing as a 45 to 125 set of XL's or HiBeams or SwingBass, even though the guages are exactly the same. Even slight changes in guage/brand are completely different as far as intonation is concerned.
The Black Art of String Winding covers metallurgy, the core thickness, the wrap(s) thickness, the wrap tension, hand wound/machine wound, round core, hex core, and on and on: This is why a Boomer .45 and a Deep Talkin' Bass .45 and an XL .45 are all very different animals, feel-, tension-, and intonation-wise.
J o e y