Do transfer students get left behind? I'm a student in the mathematics department that's close to graduation and I've TA'd a few classes and been around.

One thing I've noticed is that a lot of professors in these junior and senior level courses seem to put transfer students on the back burner. Maybe it's because they didn't get to form early bonds with them in their freshman and sophomore years. They just don't seem to be treated the same or maybe just not as involved in classes.

One thing I can say for certain, though, is that our "Orientation Day" for transfer students is weak and petty compared to the one for new college students. Is this common for transfer students to sometimes get lost in the dust, unequal opportunities, or simply different treatment? Clearly universities have an interest and a phenomena does exist because they send out "Transfer Student Survey"'s all the time, so the colleges are aware that something is different.
It depends on the school. My undergrad institution, for example, went out of the way to try to pull transfer students into the fold. While I was not a transfer student, I worked closely with the orientation department and this was a big push on their part. However, it usually comes down to the individual student. I suspect that many transfer students are perhaps overly self-restrained upon transferring to a new school and thus don't reach out enough. So, as @RoboKaren pointed out in the comment above, transfer students are often left behind.

A great piece of advice I was given about college (and grad school) in general was "you're paying for it so get your money's worth." I admit this doesn't perfectly translate outside the US where you may not be paying for it directly, but the sentiment is the same. You're spending your time (and possibly money), so be proactive. Ask questions, make a concerted effort to get to know the professors, etc. Faculty probably couldn't care less that you transferred as long as you're interested and/or talented in their pet field. If you make a clear effort to do this, whether or not you're a transfer student will make zero difference.