Regarding your first question -- Recruiters probably discount online MBAs, for a few of reasons 1) For the most part the admissions process isn't as rigorous as EMBAs, Full-time or Part-time 2) Online MBAs lack the student interaction and therefore the building of teamwork skills that recruiters seek and 3) Online MBA programs are still seen as less rigorous programs -- perhaps this will change in the future.
Regarding your second question -- This isn't a big deal at all. They might ask why you returned to your undergrad school, but as long as you have a decent answer you're fine. There are several students who do their MBA at their undergrad institution and it doesn't effect their recruitment.