I think the negative connotation you've picked up on has less to do with the university as it does with the overall career path. It's a question of whether the graduate degree was a serious endeavor and a new chapter in your career, or just "sticking around another semester."
A lot of schools now are doing this combined BS/MS thing where you can double-count your electives as both graduate and undergraduate. The end result can be literally nothing more than one more semester in school. I don't consider that a second degree, I consider that graduating with honors. If, on the other hand, you get a 4 year degree and then go the traditional graduate school approach, taking an additional 10 credits of graduate classes over 2 years while working, either for the university or for some other company, now you did 2 separate things, and therefore are worth more.
The point is that it isn't "from the same school" or "from two different schools", it's that the combined BS/MS thing is sold to students as a shortcut, and employers know it's a shortcut. An applicant with 5 years of school (combined BS/MS) and no experience, is less desirable than a candidate that did 4 years of undergrad and then did an additional 2 years of graduate classes plus research / TA / working.