Rapport behaves pretty much like a trojan. I never tried it, someone who has tells me it is difficult to remove (because like a trojan it doesn't want to be disabled or removed).
Now they want it to collect data and phone home, looking even more like malware.
All these add on security things are going to conflict with measures you take to avoid what they try to protect you from. I notice Halifax online banking has some invisible Flash things which I assume are some attempt at enhanced security but my enhanced security blocks them anyway.
If I was really worried about online banking security (and maybe I should be) then VMWare player and a little appliance dedicated to the task seems like a good solution, sadly with all the crap banks put on the web pages it would probably need one of the 'big' browsers with their big set of vulnerabilities.