I’m having the same problem. Everything was great before the last WP Remote update. I manually updated all my sites. Now on plugins that need to update … I click the update button and WP Remote appears to work its magic but the plugin doesn’t update.
Opening WP for the sites and updating that way works fine.
Here are the problematic plugins for me: Soliloquy Lite, Options Framework and Simply Instagram.
Thanks for a great plugin and I’m sure it will be fixed.