I'm using console port with steam controller, bindings are provided by steam in big picture mode.

While controller is intact and other buttons are generally fine, including LT+RT modified actions, sometimes RT as exclusive modifier stops working and interface restart does not help. I use bartender 4 to modify panel layout.

Also I have noticed if spell bound to Y procs, I cannot start combat with it, at first I need to enter combat with another spell.

Second issue happens to different keys, for some reason they are unusable from outside of combat mode(until I enter combat with any different skill)

Where can I find an official template for a steam controller btw? maybe I have just configured it wrong way

Are you using a custom interface?

Here's the profile anyway:
http://forums.consoleport.net/index.php?action=dlattach;topic=6.0;attach=5

The RT-issue you speak of doesn't have to do with the addon, since the addon only responds to the controller. It can't simply omit the input of a modifier. Something is wrong either with your controller or the profile, although I never ran into this issue with the official template.

I don't understand your second issue in the sense that there's nothing special about Y in particular. You'll have to provide information about what it's bound to, in what situation it happens and whether you're using Y as any of the interface cursor inputs.

Just bartender4 for panels. Also maybe worth mentioning that I'm using wine to run wow, maybe that's the problem?

Tried disabling bartender, seems to be cause for both problems.