Works now, needed some tweaking
It appears the "bug" if I dare to call it that, was not with Bloat Manager but rather with Launcher Pro.
If you are using the "Hidden Apps" feature of Launcher pro, you will get this weird behaviour. (I had all the bloatware already on that list)
I guess is related to LP having to keep a list somewhere of the apps and having to know they are there to be able to hide them. (hiding in LP context does not mean the app wont run, it just keeps it out of the app drawer). Haven't had time to look at the codes, and might be getting too old to do it, so I found the workaround manually:
I had to uninstall Launcher Pro, reboot, run Bloat Manager, re-install Launcher Pro and everything works fine now.
Just my two cents in case someone has the same issue...phone runs great now!!