I assume you're still trying to do train, right? VMEX seems to run out of memory or something (notice the last line you get when decompiling train is a blurb about memory allocation in java or something like that) when decompiling the overlays (too many of them? No idea... all I know is that most HL 2 maps Valve uses infodecals rather than overlays, so I think that is, in fact, the problem).
At any rate, you can salvage what the decompiler does decompile by opening up de_train_d.vmf with notepad (or any text editor) and adding a "}" at the end. I deleted the last overlay in the file, because it was incomplete, but I'm not sure if that's neccessary.
I haven't e-mailed the VMEX guy about the problem yet, but somebody should...
*edit* Typos, and I really wish this forum worked with Opera 