Yes, bad evaluations follow you when transferring programs. All you can do is put your best foot forward. Be able to explain why the evaluations were not good or inaccurate and are an anomaly. As you say, that people may be bitter you are moving on is one such reason someone might sabotage you. Sometimes programs are malignant, we all know that. At the same time, try to get some additional letters/evaluations that you can provide. It is difficult, but such things can be overcome with a positive and humble attitude.
Example: I had a professor write a sealed letter sabotaging me back when I applied to med schools. My biochemistry professor wrote "I'm not sure if wolfvgang22 is lazy or not intelligent enough to earn an A in biochemistry." (By the way, I earned an 87 in that biochem class, congruent with my 3.87 undergrad GPA.) I later learned the guy was bitter because he never got into med school and was struggling to get tenure in biochemistry and did the same to a few other applicants. I had no idea he would sabotage me at the time. Fortunately, all my other letters were positive and med school admissions smelled a rat and asked me about the quote, and I was humble and positive, not defensive when asked about it. Yes, that professor was invited to my med school graduation. No, he didn't attend. Yes, the ******* is still an advisor to pre-med students.
