When I hit the "Check for Updates" it will download v0.9.10, but then corrupt file and will not restart.
I have to re-install to use again.

Yeah.. that's entirely windows' fault sadly; doesn't happen in Linux and I doubt it happens on Macs. I will remove that feature soon because WebStart always makes sure you're running the latest. I'll replace the "downloadable" version by a shortcut to the WebStart so you don't need to open a browser whenever you need to start it.

but then wouldn't that change the settings to your web start version?
and when will there be a full download of version 0.9.10?

I like the java version only because it seems to be the only one that actually checks addons and downloads them right.
UniUploader lists all addons whether they are current or not.. and doesn't seem to download or install them.

The only thing I find lacking in 0.9.9 is a password option, for uploading guildprofiler.lua

jUniUploader started with WebStart or started by installing it manually both use the same configuration; no settings are lost by switching between either method. WebStart just keeps you nicely up to date without any negative effects in Windows.

jUniUploader isn't really a java version of UniUploader; it's a program made completely separate from UniUploader that happens to do mostly the same things.

You can specify a password for uploading guild members already. This is done with the Additional Post Variables box. Its tooltip should explain what you need to do properly.