I recall that one time, with an earlier O/S than I have on my BB now, I was doing a backup. The checkboxes behaved in a way that I thought seemed backwards. Either my apps were checked, and it looked like if I left them checked (in the Desktop Manager...app loader...backup...can't remember which one I was using at the time), and hit the 'Next' button, they kept getting listed as apps to be uninstalled. If this is ringing any bells for you, try going to the previous step, and whatever you're doing with the checkboxes for these apps, try the opposite, and hit the 'next' button.
Sounds like you've already resolved your issue about having not installed "Handheld Software". For those of you complaining about "no system software", there's the Desktop Manager, and then, once you have Desktop Manager running, you have to find the "Handheld Software" for the device you're using. The version of the handheld software does not automatically equal the version of the Desktop Manager software. You have to manually install the right version in both places.
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