True, uninstalling the BlackBerry Desktop Software, then restarting your computer, then installing it again, then installing the new OS usually solves this problem
Here is what just happened with me (maybe this helps)
I wiped my phone completely using BBSAK. Then I installed 353 and shrunk it, but when I launched apploader, it did find my phone's PIN, but it says no software was available for your device.
What I did then, I installed the official 296 again, then manually deleted its folder from:
C:\Program Files (x86)\Common Files\Research In Motion\Shared\Loader Files
I deleted the folder of 296 as I didn't want loader.exe to install that OS, I left the 353 alone though.
This time, when I launched loader.exe, it was able to install 353 just fine