Some materials built into the game do not use the map's cubemaps for reflections, and instead use a custom cubemap. To my mind all Australium weapons do this, and some of the MvM museum props.
If a map file does not contain any cubemap VTFs, but it does contain env_cubemap entities, then the game will either use the default Half-Life 2 sunset cubemap, or sometimes reflect the black and purple checkerboard pattern. In my experience, players with integrated graphics chips tend to experience the latter.
So with this in mind it seems that cubemaps are not being built for your map.
It's important to note that the cubemap building process takes place in the game, and is not a part of the compile process involving VBSP, VVIS and VRAD. If you have followed the steps of the linked guide, but you still do not see proper reflections, then there must be something causing the build process to fail. The game's console may indicate the problem. You should check the contents of the BSP to see if it contains cubemap VTFs.
Are you by any chance using Pakrat to pack custom content into the map prior to building cubemaps?