I know nothing about Wine but
1. Sounds like the Alt key is stuck.
⦁ The hotkey Alt+Delete toggles transparency for labels. (introduced in v3.6.26.4)
2. Possibly related to the stuck keys... ? Do chat commands work?
⦁ [CS] It is now possible to ignore players during the game using the /ignore and /unignore commands (in addition to the /ex and /inc commands, and using Ctrl+F1...F6).
3. Not sure what you wanted to say with the first sentence, but the frontend really is 640x480, that's not a bug. The rest I have nothing to say about.
Edit: IDK, the game's taskbar icon is supposed to flash in such cases.