I would like to do a second masters, because I would like to change focus to a certain subfield within my field (not changing fields) and have the best shot of getting into my favourite program. I also had some personal problems both during my BA and my first MA, and think I could do much better.
I am worried though that having 2 masters will set the bars slightly higher for me in the application process. Is this true? Phrased differently: are admissions people more likely to look at the my CV in a 'absolute' way, or do they judge it 'relative' to the amount of time spent in academia maybe?
In the parts of academia I'm most familiar with (mathematics, US), even one master's degree is not a necessary prerequisite for a PhD program. Some students do improve their application and chances by doing a separate master's degree, but (when a master's degree is not a necessary prerequisite) I would advise any student to also apply for PhD programs and see what they get into.
In your case, having completed one master's degree in your field and having the desire to go on to a PhD program, I think you should certainly apply to PhD programs. If there is a second master's program that you are extremely excited about -- in particular that you think is prestigious, would improve your academic record and offer you critical new skills that you would not necessarily pick up in the PhD program -- then you should apply to it as well.
If you get into a solid PhD program with funding, I advise you to take that over any master's program. This is your life, and at some point you will want to have your student days behind you while you are still somewhat spry. However, if you get in only to PhD programs that are substandard and you get into a very good master's program, then yes, taking that is probably a good investment for the future.
All this is definitely something to discuss with your current thesis advisor, by the way.