Transferring out of a Masters I am planning to complete a Masters in Physics (thesis based research) at my undergraduate institution after being rejected during PhD applications. I feel like this will bolster my research experience and strengthen my research application. After this, I plan to apply to PhD programs, both at my home institution and at other schools. Do PhD admissions committees favor a Masters degree with research? Did I make the right decision in going for a Masters?
In my own field (neuroscience) I don't think a masters really counts for anything in US PhD admissions (but these decisions are all made by humans on an admissions committee; maybe one of those humans reviewing your application likes a masters degree). Research experience you gain while doing a masters is valuable, however, it just doesn't matter that it's part of a masters program rather than a job or anything else. Sometimes a masters is the best access a recent grad has to research, though.
Unlike what Buffy's answer implies, in my field having a masters doesn't change where you are on the PhD track - you'll have just as many years and courses as someone coming in with a BS.
I can't say whether you made the right choice or if it will work out for you - no one can - but if you can gain experience in research and work with people that can write you strong letters of recommendation then this choice will increase your chances of PhD admissions. Whether it will get you into the program you want (or any program) can never be guaranteed, though.