1 pointDownload the latest GUI on the website, you should be prompted that there is an update. Macs are the only reliable machines at notifying of an available update. Let me know if that helps.
1 pointAre you trying to use your original TV remote you're using to also control your TV, to also control your HTPC? Does this remote has any universal remote control capability? If not then both your TV and HTPC (through Flirc) will see the same signal and react to it - both devices may execute some actions upon pressing some buttons.
1 pointCan you elaborate what this means: "It seems to be getting confused and not registering any keys properly... Other remotes that aren't connected to my TV work fine." Make sure you're on the latest firmware. We're on v4.4.2, and that has some fixes for sony remotes.