Hey guys I know this is an old post but like a week ago I downloaded this tool and had the same prob that malyczolg had, so I decided to look inside the .map file and found the solution to run every map without errors.
First of all I must thank Daevius and Codemanx for making such a great work with this program that helped me to recover some of my lost maps.
Open the map with notepad++ or any other programming tool. You will see these lines (for this example I'm going to use Area 51 map, made by .complex Matty)
Now, hit Ctrl+F (searching tool), insert these values and hit the "Replace all" button."The Map" flags expanded
"Brushes" flags expanded
"Brushes/Tools" flags
"Triangles" flags expanded
"Entities" flags expanded
"Entities/Models" flags
"Entities/Spawns" flags
Do the same for the rest ("Brushes/Tools","Triangles","Entities","Entities/Models","Entities/Spawns"), and after you have replaced all of them, delete the lines at the begginning of the .map (the ones I have quoted).Search: layer "Brushes"
Replace with: <leave this box empty>
Now you will avoid the "ParseEntity" error, but in Radiant you will see that any brush or curve/terrain patch will be covered with Caulk triangles (as seen in the image below).
To delete these triangles, hit the F key (filter menu) and uncheck these boxes, so you will only see those caulk triangles, like this:
Now make a BIG brush that will enclose all the caulk patches and do right click on 2D view -> Select -> Inside, so Radiant will select every object inside the square you made (this may take a while). After this, hit the Backspace key to delete them all, hit F and check the boxes again.
And you will get your decompiled map working