I haven't run into issues with Vista and POI Loader. With Vista you do often need to go into properties (by right-clicking) and tell Vista to trust the program.
Also, I have found that Vista's Compatibility Mode works pretty well. If you are still having any trouble, right click on the installation.exe for POI Loader and run it under XP compatibility. It will install and run as if you were still on XP.
... "there was a problem transferring your custom POI's to your device Please try running POI loader again".
I have Vista home premium and have no problem. Try reinstalling poi loader with your Internet security protection closed. I have Norton 360 and it gives me all types of problems when installing new programs.
Vista in m experience has been picky; i had to reistall the POI loader and the Web updater 2x before they both worked. don't know the cause, but gpx file formats don't muck up as much as the csv format. if you don't have a preference, i'd use the gpx format.
if you rename your poi file in your gps after creating in your gps you can then add more. I have different directories in my pc for groups of poi's eg shops camps etc and then after loading I change the new poi file to the directory name I updated from. This way you can just upload the directory where the new changes are and not destroy all the others. Easy to do after a couple of tries. Easier than downloading all again especially if you use proximity warnings etc.