I ran into the disappearing VAB menu bug as well. Drove me nuts these past few days trying to pin point what was causing it as I'm running heavily modded (just got a new computer and wanted to see what it could handle).
When I put in the .dll that is first suggested the bug goes away and I get the VAB menu icons back. But if I download and install the new V1.3 update then I lose the VAB menus again. I only didn't try the V1.4 because its a test version and I didn't want to risk running into something else wonky.
Here is the log file with the menu missing (using the V1.3 download)