Windows – VLC – Close/minimise buttons missing

You need to open in VLC the cue file that came with the flac, rather than the flac file.
If it's missing, that might be one reason that VLC is having problems detecting the multi-tracks.

If VLC still doesn't work even when the cue file is opened, see:

Split lossless audio (ape, flac, wv, wav) by cue file in Ubuntu
Split APE and FLAC Files in Ubuntu and Add Tags by Cue File

Known bug : Ticket #3828 (new defect) : QT4 sends processed hotkey events forward, opened 4 months ago :

There is a bug in VLC 1.1.0 QT4 interface that causes processed hotkey events to forwarded. So if volume up key from keyboard is pressed, VLC raises the volume, but it also sends same hotkey event forward and because of this Windows Mixer also raises volume.

Same applies to mute, so both VLC and Windows Mixers are muted. Right way would be that VLC eats all hotkey events it has processed and forwards only those, that it doesn't process.

The only solution is to add your voice to this bug and in the videolan forums, until it's fixed.
Or, as VLC is open source, get the sources and fix the bug, which should be simple enough.

We need more info, such as your operating system and what are the volume keys on your laptop, and what do they generate.

However, you can still try to go into VLC Preferences, Hotkeys section, click on Volume up(down), and try to set or Clear their local and global key definitions. It would be interesting to know what effect this has on the problem.