I just installed Flashtool-0.5.0.0beta-setup.exe (https://github.com/downloads/Androxyde/Flashtool/Flashtool-0.5.0.0beta-setup.exe) in Wine 1.3.33 on my Fedora Linux host. Then I ran this command from my Linux bash shell: wine C:/FlashTool/FlashTool.exe A window popped up and is running now, titled "SonyEricsson Xperia Flasher by Bin4ry & Androxyde". I can interact with it, though I don't have any phone to plug in. It sounds like you didn't get this far. Are you sure that 1.1.44 is the latest version of Wine that you have available?
